FINAL RECOVERY PLAN 

for 

JOHNSON'S SEAGRASS 

(Halophila johnsonii Eiseman) 

prepared by the 

Johnson's Seagrass Recovery Team 

for the 

National Marine Fisheries Service 

National Oceanic and Atmospheric Administration 

September 2002 

Approved: ,&&&- -7-s&-& 

National Marine ~isheriei Service 

National Oceanic and Atmospheric Administration 
i

Disclaimer

This recovery plan for Halophila johnsonii Eiseman (Johnson's seagrass) has been

approved by the National Marine Fisheries Service. It does not necessarily represent

official positions or approvals of cooperating agencies nor the views of all individuals

involved in the plan's formulation. The National Marine Fisheries Service has

determined that the information used in the development of this document represents the

best scientific and commercial data available at the time it was written. The Recovery

Plan was prepared by the Johnson's Seagrass Recovery Team to delineate reasonable

actions that will promote protection of Johnson's seagrass. This plan is subject to

modification as dictated by new findings, changes in species status, and completion of

actions described in the plan. Goals and objectives will be attained and funds expended

contingent upon agency appropriations and priorities.

Literature Citations should read as follows:

National Marine Fisheries Service. 2002. Recovery Plan for Johnson's Seagrass

(Halophila johnsonii). Prepared by the Johnson's Seagrass Recovery Team for the

National Marine Fisheries Service, Silver Spring, Maryland. 134 pages.
1

amended 1976, 1978-1980, 1982, 1986, 1988. 

ii

Preface

Congress passed the Endangered Species Act of 19731 (16 U.S.C. §§ 1531-1544)(ESA),

finding that (1) various species of plants and animals in the United States have been

rendered extinct as a consequence of economic growth and development untempered by

adequate concern and conservation and, (2) other species of plants and animals have been

so depleted in numbers that they are in danger of or threatened with extinction (16 U.S.C.

§ 1531(a)). The purposes of the ESA are to provide a means whereby the ecosystems

upon which endangered species and threatened species depend may be conserved, to

provide a program for the conservation of such endangered species and threatened

species, and to take such steps as may be appropriate to achieve the purposes of the

treaties and conventions set forth in section 1531(a) (16 U.S.C. § 1531(b)). The National

Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (USFWS) share

responsibility for the administration of the ESA. NMFS is responsible for most marine

and anadromous species including Johnson's seagrass.

Section 4(f) of the ESA directs the responsible federal agency to develop and implement

a recovery plan, unless such a plan would not promote the conservation of a species. 

NMFS determined that a recovery plan would promote conservation and recovery of

Johnson's seagrass. The Johnson's Seagrass Recovery Team included seagrass and

management experts from academia and the state and federal governments. 

The NMFS agrees with the Johnson's Seagrass Recovery Team that the goals and

objectives of this recovery plan can be achieved only if a long-term commitment is made

to support the actions recommended here. Achieving these goals and objectives will

require the cooperation of state and federal government agencies as well as private

individuals and organizations. 

NMFS and the U.S. Fish and Wildlife Service will soon publish new draft guidance on

recovery planning. This recovery plan was drafted before the draft guidance was

available and, therefore, is not written to conform with this new guidance. This recovery

plan has been under development for a long time and NMFS has decided to publish this

recovery plan without further delay.
iii

Johnson's Seagrass Recovery Team:

Layne Bolen, Protected Resources Division, NMFS, Southeast Region, Panama City

Field Office, Panama City, Florida. 

Robert Brantly, Office of Beaches and Coastal Systems, Florida Department of

Environmental Protection (FDEP), Tallahassee, Florida. 

Dr. Michael Durako, Center for Marine Science Research, University of North CarolinaWilmington, Wilmington, North Carolina.

Dr. Penny Hall, Marine Research Institute, Florida Fish and Wildlife Conservation

Commission (FWC), St. Petersburg, Florida.

Dr. Jud Kenworthy (Team Leader), National Ocean Service (NOS), National

Oceanographic and Atmospheric Association (NOAA), Beaufort Lab, Beaufort,

North Carolina.

Dr. Herb Kumpf (Team Leader), Panama City Field Office, NMFS Southeast Fisheries

Science Center, Panama City, Florida. 

Keith Mille, Office of Beaches and Coastal Systems, FDEP, Tallahassee, Florida. 

Lori Morris (Alternate), Division of Environmental Services, St. Johns River Water

Management District (SJRWMD), Palatka, Florida.

Marta Nammack (Team Advisor), Office of Protected Resources, NMFS, Silver Spring,

Maryland. 

Stephen Traxler, Planning Division, U.S. Army Corps of Engineers (COE), West Palm

Beach, Florida.

Dr. Robert Virnstein, Division of Environmental Services, SJRWMD, Palatka, Florida.
iv

Table of Contents

Disclaimer ........................................................ i

Preface .......................................................... ii

List of Figures and Tables ............................................ vi

List of Abbreviations ............................................... vii

Executive Summary ................................................ viii

1.0 BACKGROUND ................................................. 1.0-1

1.1 Taxonomy ................................................. 1.1-1

1.2 Population Size and Distribution ................................. 1.2-1

1.3 Growth Form and Reproductive Biology ........................... 1.3-1

1.4 Ecological Role of Halophila Johnsonii ........................... 1.4-1

1.5 Current Status and Historical Conditions ........................... 1.5-1

1.6 Critical Habitat .............................................. 1.6-1

1.7 Reasons for Listing ........................................... 1.7-1

1.8 Listing Determination ......................................... 1.8-1

1.9 Conservation Measures ....................................... 1.9-1

1.9.1 Federal Conservation Measures ......................... 1.9-1

1.9.2 State of Florida Conservation Measures ................... 1.9-4

1.9.3 Summary of Conservation Measures ..................... 1.9-16

2.0 RECOVERY STRATEGY .......................................... 2.0-1

3.0 RECOVERY OF JOHNSON’S SEAGRASS ............................ 3.0-1

3.1 Objectives and Criteria ........................................ 3.0-1

3.1.1 Revision of Recovery Criteria ........................... 3.0-1

3.2 Recovery Program .......................................... 3.2-1

Action 1. Identify and protect populations and habitat ............. 3.2-1

Action 2. Initiate a range-wide monitoring program ............... 3.2-3

Action 3. Refine habitat requirements of Halophila johnsonii. ....... 3.2-7

Action 4. Conduct detailed life history studies of Halophila 

johnsonii to examine vegetative fragment dispersal, 

survival, and sexual reproduction. ...................... 3.2-9

Action 5. Determine and implement habitat management needs and

techniques ....................................... 3.2-10

Action 6. Identify the genetic diversity and genetic structure of 

Halophila johnsonii across its geographic range. .......... 3.2-15

Action 7. Develop restoration techniques ...................... 3.2-16

Action 8. Formulate an educational outreach program to increase

awareness of Johnson’s seagrass and its status. ............ 3.2-18

3.2.1 Recovery Action Summary .................................. 3.2-21

4.0 IMPLEMENTATION SCHEDULE ................................... 4.0-1

4.1 Halophila johnsonii Implementation Schedule ....................... 4.1-1
v

4.2 Implementation Schedule Summary ............................... 4.2-1

5.0 REFERENCES ................................................... 5.0-1

APPENDIX I. Listing Notice for Halophila johnsonii

Federal Register 63(177): 49035 ................................... A.I-1

APPENDIX II. Notice for Critical Habitat for Halophila johnsonii

Federal Register 65(66): 17786 .................................... A.II-1

APPENDIX III. Recommendations for sampling Halophila johnsonii

at a project site ............................................... A.III-1
vi

List of Figures and Tables

Figure 1. Halophila johnsonii. Leaves are generally 2-5cm long. (Adapted from

Eiseman and McMillan 1980) ............................................ 1.1-3

Figure 2. Geographic Range of Halophila johnsonii. Sebastian Inlet to northern 

Virginia Key ........................................................ 1.2-2

Table 1. Morphological, reproductive, and genetic characteristics of H. johnsonii

and H. decipiens ..................................................... 1.1-4
vii

List of Abbreviations

ASMFC Atlantic States Marine Fisheries Commission

CARL Conservation and Recreation Lands

CCP Coastal Construction Permit

COE U.S. Army Corps of Engineers

DGPS Differential Global Positioning System

EFH Essential Fish Habitat

EPA Environmental Protection Agency

ERP Environmental Resource Permitting

ESA Endangered Species Act

F.A.C. Florida Administrative Code

FDACS Florida Department of Agriculture and Consumer Services

FDEP Florida Department of Environmental Protection

FFA Florida Forever Act

FWC Florida Fish and Wildlife Conservation Commission

FNAI Florida Natural Areas Inventory

FR Federal Register

F.S. Florida Statutes

GIS Geographic Information System

HCD NMFS/ Habitat Conservation Division

IRL Indian River Lagoon 

IRLCCMP IRL Comprehensive Conservation and Management Plan 

IRLNEP IRL National Estuary Program 

JCP Joint Coastal Permit

MSSW Management and Storage of Surface Waters Program

NMFS National Marine Fisheries Service

NOAA National Oceanographic and Atmospheric Association

NOS National Ocean Service

OFWs Outstanding Florida Waters

PAR Photosynthetically Active Radiation

PLRGs Pollution Load Reduction Goals

SAFMC South Atlantic Fishery Management Council

SAV Submerged Aquatic Vegetation

SJRWMD St. Johns River Water Management District

SFWMD South Florida Water Management District

SWIM Surface Water Improvement and Management Act 

TMDLs Total Maximum Daily Loads

WMDs Water Management Districts

WR Wetland Resource Permit Program

USCG United States Coast Guard

USFWS United States Fish and Wildlife Service
viii

Executive Summary

Current Species Status: Johnson's Seagrass (Halophila johnsonii Eiseman) was listed

as threatened on September 14, 1998 (63 FR 49035): the first marine plant species to be

listed under the ESA. Critical habitat for Johnson's seagrass was designated on April 5,

2000 (65 FR 17786). Halophila johnsonii has been found growing only along

approximately 200 kilometers (km) of coastline in southeastern Florida between

Sebastian Inlet and north Biscayne Bay. The species is rare, has a limited reproductive

capacity, and is vulnerable to a number of anthropogenic and natural disturbances.

Habitat Requirements and Limiting Factors: Where present in its limited geographic

range, H. johnsonii often grows in a patchy, non-contiguous distribution at water depths

extending from the intertidal down to 3 meters (m). Halophila johnsonii appears to

reproduce only through asexual branching. Principal threats to the species' survival

include: 1) habitat degradation and destruction from dredging and filling, construction

and shading from in- and overwater structures, prop scarring, altered water quality, and

siltation; 2) inadequacy of existing regulatory mechanisms to protect seagrasses; and 3) 

stochastic storm events.

Recovery Goal: To delist Johnson's Seagrass and to assure its persistence throughout its

range. 
ix

Recovery Objective and Criteria: Halophila johnsonii should be considered for

delisting when the following conditions are met: 1) The species’ present geographic

range remains stable for at least 10 years or increases, 2) Self-sustaining populations are

present throughout the range at distances less than or equal to the maximum dispersal

distance to allow for stable vegetative recruitment and genetic diversity, and 3) 

Populations and supporting habitat in its geographic range have long-term protection

(through regulatory action or purchase acquisition).

Actions Needed:

1. Identify and protect populations and habitat.

2. Initiate a range-wide mapping and monitoring program.

3. Refine habitat requirements of H. johnsonii.

4. Conduct detailed life history studies of H. johnsonii to examine vegetative fragment

dispersal, survival, and sexual reproduction.

5. Determine habitat management needs and techniques.

6. Identify the genetic diversity and genetic structure of H. johnsonii across its

geographic range.

7. Develop restoration techniques.

8. Formulate an educational outreach program for H. johnsonii and seagrass habitat. 

Cost of Recovery Actions: The exact costs of recovery and protection are

undeterminable at this time. Refer to the Implementation Schedule for cost and time

estimates for individual actions. Cost estimates were not available for some actions
x

because the actual procedures for accomplishing these actions are not yet known. In

addition, many of the actions are linked to one another so that accomplishing one may

allow for others to be concurrently achieved. Therefore, exact costs were impossible to

predict.
1.0-1

1.0 BACKGROUND

The seagrass Halophila johnsonii Eiseman (Johnson's seagrass) is a rare plant that may

have the most limited distribution of any seagrass on earth. It frequently occurs in small

(centimeters [cm] to a few m diameter) isolated patches. Unlike most Halophilas, which

can survive perturbations by using sexual reproduction to disperse and maximize

offspring, H. johnsonii appears to reproduce only through asexual branching or apomixis

(Eiseman and McMillan 1980). There are no known seed banks; and although

experiments have shown that vegetative fragments survive when transplanted into the

field and in experimental mesocosms, there is only circumstantial evidence for unassisted

recruitment by naturally produced fragments. Thus, the plant has a reduced capacity to

repopulate an area if lost due to human or environmental perturbations. The apparent

lack of sexual reproduction suggests this species may have limited genetic diversity. 

Because of its small size and minimal stored reserves, local populations of H. johnsonii

may decline during periods of unfavorable conditions, be out-competed by larger

seagrasses, or become overgrown by macroalgae. Halophila johnsonii is particularly

vulnerable to sediment disturbances, trampling, and prop scarring due to its fragile nature

and predominantly shallow growth habit; and, for these reasons, it will have a limited

recovery potential.
1.1-1

1.1 Taxonomy

Presently, there are 12 recognized species of seagrass in the genus Halophila (den Hartog

1970). The genus is distributed in warm-temperate and tropical waters worldwide; the

only pan-tropical species is Halophila decipiens Ostenfeld. All species of Halophila are

morphologically distinguished from the other seagrass genera by having either a pair of

leaves or a pseudowhorl of leaves at each rhizome node. Most Halophilas are small,

shallow rooted, and have 2-3 orders of magnitude less biomass per unit area compared to

other seagrass genera. Although small, biomass turnover rate is relatively high, and the

plants decompose quickly (Kenworthy et al. 1989). 

Diagnostic Characteristics of Halophila johnsonii

After many years of confusion over identification, H. johnsonii was formally proposed as

a separate species by Eiseman and McMillan (1980). Halophila johnsonii was

previously referred to either as H. decipiens or H. baillonis Ascherson, but it most closely

resembles H. ovalis (R. Brown) Hooker f., an Indo-Pacific species, both morphologically

and genetically (McMillan and Williams 1980). Plant classification schemes based on

anatomical (den Hartog 1970) and molecular phylogenetic (Les et al. 1997) methods both

place the seagrass genus Halophila in the angiosperm family Hydrocharitaceae, along

with two other seagrass genera, Thalassia and Enhalus. Morphologically, Johnson’s

seagrass is recognized by the presence of pairs of linearly shaped foliage leaves, each

with a petiole formed on the node of a horizontally creeping rhizome (Figure 1). The

rhizome is located at or just below the sediment surface and is anchored to

unconsolidated substrate by unbranched roots. The leaves are generally 2-5 cm long
1.1-2

(including the petioles), and the rhizome internodes rarely exceed 3-5 cm in length,

making this species appear diminutive relative to the larger seagrasses. H. johnsonii

differs from H. decipiens in a number of morphological, reproductive, and genetic

characteristics (Table 1). The diagnostic characteristics of H. johnsonii remain
1.1-3

F

FLOWER

FRUIT

APICAL MERISTEM

Figure 1 (See Table 1). Halophila johnsonii. Leaves are generally 2-5 cm

long. Adapted from Eiseman and McMillan (1980). 
1.1-4

Table 1. Morphological, reproductive, and genetic characteristics of H. johnsonii

and H. decipiens.

H. johnsonii H. decipiens

Linear leaves with entire (smooth)

margins.

Oblong-elliptical leaves with serrate

margins.

No hairs on blade surface. Unicellular prickle hairs on both surfaces

(unique to H. decipiens).

Leaf cross veins diverge at ca. 45o angles. Leaf cross veins at ca. 60o angles.

Only pistillate (female) flowers are

known so it is possibly dioecious (male

and female plants) or apomictic (produces

seeds without pollination or meiosis so

seeds are clones of female parent).

Monoecious (both sexes on one plant).

Populations of H. johnsonii collected in

the Indian River Lagoon (IRL) differed

from H. decipiens in five isozymes of the

seven isozyme systems tested, with major

differences in three of the enzymes

(Jewett-Smith et al. 1997).

See box at left.

Illustrations adapted from Phillips and Menez,1988.
1.1-5

relatively unchanged when plants are cultured in artificial conditions; thus, differences

between the two species are not due to phenoplasticity.
1.2-1

1.2 Population Size and Distribution

Although the genus Halophila has one of the most extensive distributions of all the

seagrasses, H. johnsonii has only been found growing in lagoons along approximately

200 km of coastline in southeastern Florida between Sebastian Inlet and north Biscayne

Bay (Figure 2). This narrow range and apparent endemism indicate that H. johnsonii has

the most limited known geographic distribution of any seagrass in the world.

Species of Halophila are documented to occur from intertidal to 85 m depths (may be the

deepest growing seagrasses); shallow occurrence is frequently associated with high

turbidity. Halophilas regularly occur in 30-40 m depths, thus are important contributors

to primary production of coastal shelf environments (e.g., extensive beds on the West

Florida Shelf). Some species are the primary colonizers of disturbed environments,

apparently due to their tolerance to low light, their high sexual fecundity, and their rapid

horizontal growth rates. Unassisted recruitment by vegetative fragments has never been

documented for any Halophila species (Heidelbaugh et al. 1999). 

In the IRL, H. johnsonii is one of the least abundant seagrass species (Virnstein et al.

1997). Within Johnson’s seagrass’ distributional range, the least abundant species is

Halophila engelmannii Ascherson; however, H. engelmannii has a much wider
1.2-2

Figure 2 Geographic range of Halophila johnsonii: Sebastian Inlet to northern Virginia Key

(Kenworthy 1997). 
1.2-3

geographic range, including the Bahamas, Florida, Cuba and the Gulf of Mexico

(Kenworthy 1997). Halophila johnsonii often grows in a patchy, non-contiguous

distribution at water depths extending from the intertidal down to 3 m (Kenworthy 1993;

Virnstein et al. 1997). Intertidal populations may be completely exposed at low tides,

suggesting tolerance to dessication and wide temperature ranges. The largest known

contiguous distribution of patches occurs near the northern (Sebastian Inlet) and central

range of this species (Lake Worth). Although it is more commonly found in monotypic

patches, Johnson’s seagrass can also occur among low-to-moderate densities of Halodule

wrightii Ascherson and Syringodium filiforme Kutzing, and mixed with H. decipiens in

deeper water.

Observations of its distribution and the results of some very limited experimental work

suggest that H. johnsonii has a wider tolerance of salinity, temperature, and optical water

quality conditions than H. decipiens (Dawes et al. 1989). Documented salinity range is

15-43 parts per thousand (ppt) (physiological salinity tolerance range may be greater;

Dawes 1989; Virnstein et al. 1997) and the species has been observed growing

perennially near the mouths of freshwater discharge canals (Gallegos and Kenworthy

1996). Although specific thermal tolerances for growth and mortality have not been

determined, observations indicate that Johnson’s seagrass grows all year long at its

northern range limits near Sebastian Inlet where temperatures have dropped below 10

degrees C. Johnson’s seagrass does not exhibit photoinhibition at high light intensities as

does H. decipiens, so it is found growing from deeper turbid waters of the interior portion
1.2-4

of the IRL up to the intertidal. Johnson's seagrass also grows in clear water associated

with the high energy environments and flood deltas inside ocean inlets where tidal

velocities approach the threshold of motion for unconsolidated sediments (35-40 cm 

second-1).
1.3-1

1.3 Growth Form and Reproductive Biology

Johnson’s seagrass grows vegetatively by the division of meristems located on the apex

of the horizontal rhizome and in the axial point (node) where the petioles intersect the

rhizome. As in all clonal plants, vegetative growth and areal coverage is achieved by

meristem division, the iteration of modules (leaf pairs and apical meristems), and

branching of the horizontal stem (rhizome). Since seagrasses are angiosperms, many

species also reproduce sexually; however, no male flowers have ever been described nor

is there any evidence of successful recruitment by seed for Johnson's seagrass, even with

extensive, decade-long observations. Female flowers of H. johnsonii arising from the

base of the petioles are enclosed in a two-leaved spathe. The fruits are long-necked with

3 stigmas, each 2-4 cm in length. 

There is no evidence of sexual reproduction in this species; therefore, H. johnsonii must

rely on asexual branching and clonal reproduction for maintenance and dispersal. Thus,

H. johnsonii will be at a disadvantage, particularly if extirpated from an area, compared

to either the highly fecund H. decipiens or the larger seagrasses in re-establishing after

periods of unfavorable conditions. The competitive advantage of the larger seagrasses

stems from their size and the energy storage capabilities of their comparatively larger

rhizomes, which provide a buffer during unsuitable conditions. Small species can

survive these unfavorable environmental conditions by the production of a seed bank

which allows the plants to re-emerge when favorable conditions return, but seed

production and viability are unknown for H. johnsonii. 
1.3-2

The genetic diversity of clonal plants depends strongly on the relative proportions of 

sexual versus asexual reproduction (Hamrick et al. 1979). Only asexual reproduction is

presently known for this species (because of the apparent absence of male flowers) and

little genetic variation has been documented (Jewett-Smith et al. 1997). Limited genetic

variation within, and among, patches may be possible, however, due to somatic mutation

and genetic drift (Loveless and Hamrick 1984). Preliminary surveys using Randomly

Amplified Polymorphic DNA analyses indicate that there are small, isolated populations

of H. johnsonii that have clones which are genetically distinct from clones at other

locations (Freshwater 1999). Two populations in the more southerly range of the species,

one from near Boynton Beach and a second population from Boca Raton, exhibit higher

genetic variability than populations from the central (Jupiter Inlet) and northern range

(Fort Pierce Inlet, Johns Island, Sebastian Inlet) of the species. Since there are no known

occurrences of male flowers, it is suspected that the extant populations of H. johnsonii

are maintained almost exclusively by clonal growth and asexual reproduction.

Consequently, gene flow may be severely restricted because of very infrequent or no

genetic recombination, and the current variation in H. johnsonii may be due to somatic

mutation associated with asexual reproduction and clonal growth. If this is the case,

these isolated clones serve as important reservoirs of genetic information for the species

and should be protected.
1.4-1

1.4 Ecological Role of Halophila Johnsonii

Despite its diminutive size, studies indicate that Johnson's seagrass provides similar

ecological and economic benefits to the larger seagrasses i.e., a food source, a refuge, and

nursery for numerous wildlife species, sediment stabilization, and deceleration of water

currents and waves reducing turbidity and erosion (Zieman 1982; Virnstein et al. 1983;

Phillips and Menez 1988; Fonseca 1994). Patches of H. johnsonii provide a level of

support for epiphytes and epifauna (Hodgkin and Lenanton 1981; Virnstein and

Carbonara 1985; Howard 1987; Virnstein and Howard 1987) and algae (Thompson 1978;

Virnstein and Carbonara 1985; Hall and Bell 1988; Holmquist 1994). Like other

Halophila species, because of its small size and rapid turnover rate, this seagrass is

especially important in detritus and nutrient cycling (Kenworthy 1993; Bolen 1997). 

Green sea turtles, West Indian manatees, and dugongs are known to feed on Halophila

species and this genus may represent a significant component of their diet (Bjorndal

1981; Packard 1981; Lefebvre pers. comm. 1991; Foley and Bolen 1996; Jupp et al.

1996).

If extirpated from an area, H. johnsonii will be at a disadvantage compared to either the

highly fecund or larger species in re-establishing itself due to its known lack of seed

banks and limited energy storage capabilities. However, rapid growth assists H.

johnsonii in playing an opportunistic role in the recovery of disturbed sites, and it will

stabilize the sediments of disturbed sites before the larger seagrasses can establish

themselves (Packard 1981; Fonseca 1989; Kenworthy 2000). Halophila johnsonii
1.4-2

stabilizes sediments by increasing the threshold velocity for sediment motion as has been

reported for the similar-sized H. decipiens (Fonseca 1989). 
1.5-1

1.5 Current Status and Historical Conditions

Halophila johnsonii has only relatively recently been identified as a distinct species

(Eiseman and McMillan 1980) and no historical information on the species’ distribution

is available. No monitoring program exists specifically for H. johnsonii. The most

comprehensive and quantitative distribution and abundance data comes from the State of

Florida Surface Water Improvement and Management Act of 1987 (SWIM) Project. 

Since 1994, all seagrass species have been monitored twice a year within 1-m2 quadrats

placed every 10 m along 75 fixed transects in the IRL between Sebastian Inlet and Jupiter

Inlet. The following information is based on this seagrass monitoring program (Virnstein

et al. 1997).

In the IRL, H. johnsonii is discontinuous. It occurs over a range of depths (intertidal to

1.8 m), salinities, and water quality. Halophila johnsonii was found at 20 of 33 transects

within the IRL during 1994-1997, but at not more than 12 transects at any one sampling

time. Eight of the transects were specifically located to include H. johnsonii; the species

is therefore over-represented in this monitoring program compared to random sampling. 

Where it does occur, its distribution is patchy, both spatially and temporally. It occurred

in 4.6% (106 of 2,280) of the 1-m2 quadrats sampled within the IRL. Average percent

cover (measured as shoot frequency within grid cells of the quadrat) over all sampling

dates and transects was 1.5%.
1.5-2

Halophila jonsonii is a perennial plant with no strong seasonal pattern, although it

generally exhibits some winter decline. Monitoring in the IRL indicates that there is

spatial and temporal variation in the abundance of H. johnsonii patches (Virnstein et al.

1997). Although the monitoring data are limited, no large distributional gaps have been

detected in the IRL, and there has been no overall increase or decrease in abundance or

geographic range over the period from summer 1994 to summer 1999. The recent

increase in search effort (as this plant becomes more widely recognized) may be

responsible for any apparent increase in reported occurrences.
1.6-1

1.6 Critical Habitat

The Recovery Team has identified the following critical habitat criteria for H. johnsonii: 

1) populations that have persisted for 10 years, 2) persistent flowering populations, 3) the

northern and southern limits of the species, 4) unique genetic diversity, and 5) a

documented high abundance of H. johnsonii compared to other areas in the species’

range. Based on these criteria, ten areas in the geographic range of Johnson's seagrass

were designated as critical habitat (65 FR 17768) (Appendix II). These ten areas and

their approximate acreage include: a portion of the Indian River Lagoon, north of the

Sebastian Inlet Channel (5.7); a portion of the Indian River Lagoon, south of the

Sebastian Inlet Channel (2.0); a portion of the Indian River Lagoon near the Fort Pierce

Inlet (4.3); a portion of the Indian River Lagoon, north of the St. Lucie Inlet (2770); a

portion of Hobe Sound (900); a site on the south side of Jupiter Inlet (4.3); a site in

central Lake Worth Lagoon (15.0); a site in Lake Worth Lagoon, Boynton Beach (95.5);

a site in Lake Wyman, Boca Raton (20.0); and a portion of Biscayne Bay (18,757). This

designated area accounts for approximately 22,574 acres or 9,139 hectares. 
1.7-1

1.7 Reasons for Listing

After a thorough review and consideration of all information available, NMFS concluded

that H. johnsonii warrants listing as a threatened species. Procedures found at section

4(a)(1) of the ESA (16 U.S.C. 1531 et seq.) and regulations (50 CFR part 424)

promulgated to implement the listing provisions of the ESA were followed. A species

may be determined to be endangered or threatened due to one or more of the five factors

described in section 4(a)(1). These factors and their application to H. johnsonii are:

1. Present or Threatened Destruction, Modification, or Curtailment of its Habitat or

Range.

Habitat in the limited range in which H. johnsonii exists is at risk of degradation or

destruction by a number of human and natural perturbations, including (1) dredging and

filling, (2) construction and shading from in- and overwater structures, (3) prop scarring

and anchor mooring, (4) trampling, (5) altered water quality (such as stormwater runoff

and turbidity), (6) storms, and (7) siltation. Due to the fragile nature of H. johnsonii’s

shallow root system, the plants are vulnerable to human-induced disturbances in addition

to major natural disturbances to the sediment, and their potential for recovery may be

limited. Destruction of benthic communities due to boating activities (propeller scarring

and anchor mooring) was observed at all H. johnsonii sites during a NMFS study

(Kenworthy 1993). Further, this impact is expected to worsen with the rapidly expanding

population of this region and the predicted increase in boating activity. This activity

severely disrupts the benthic habitat by severing rhizomes and significantly reducing the
1.7-2

viability of the populations. Trampling due to human disturbance and increased land-use

induced siltation can also threaten the viability of the species. 

Turbidity is another critical factor in the distribution and survival of seagrasses,

especially in deeper regions of the IRL, where reduced Photosynthetically Active

Radiation (PAR) limits photosynthesis. Shallow regions are less affected by turbidity

unless light is rapidly attenuated. In interior lagoonal areas where salinity is low, highly

colored water typically is discharged via drainage systems. These stained waters

attenuate shorter wavelengths rapidly, removing important PAR as well as potentially

stressing plants by lowering salinity. This is a critical factor in the vicinity of Sebastian,

St. Lucie, Jupiter, and Ft. Pierce Inlets, and Lake Worth and North Biscayne Bay, where

freshwater reaches the flood tide deltas and nearby seagrass meadows via rivers and

canal systems discharging into the lagoon. Under certain conditions, these effects may

also be severe at lagoonal sites farther from the inlets. 

Degradation of water quality due to human impact threatens the welfare of all seagrass

communities, including those of H. johnsonii, and subsequently affects fishery resource

productivity, in general. Nutrient over-enrichment caused by inorganic and organic

nitrogen and phosphorous loading, via urban and agricultural land run-off, can stimulate

increased algal growth that may smother the understory of seagrasses, particularly H.

johnsonii, shade rooted vegetation, and diminish the oxygen content of the water. Such
1.7-3

low oxygen conditions have a demonstrated severe negative impact on seagrasses and

associated communities. 

2. Overutilization for Commercial, Recreational, Scientific, or Educational Purposes.

Overutilization for these purposes has not been a documented factor in the decline of this

species.

3. Disease or Herbivory.

There are two known large herbivores that occur in the range of H. johnsonii—the green

sea turtle (Chelonia mydas), and the West Indian manatee (Trichechus manatus); both

feed upon the seagrass. Herbivorous fish also feed upon seagrass communities, but

herbivory pressure alone is not likely to be a threat to the species' existence. 

4. Other Natural or Human-made Factors Affecting the Species' Continued Existence.

The existence of the species in a very limited range increases the potential for extinction

from stochastic events. Natural disasters such as hurricanes could easily diminish entire

populations and a significant percentage of the species. Seagrass beds that are near inlets

are especially vulnerable to storm surge from hurricanes and severe storm events.

5. The Inadequacy of Existing Regulatory Mechanisms.
1.7-4

Despite existing federal and Florida state laws to conserve and protect seagrass habitat,

there is a continued and well-documented loss of seagrass habitat in the United States

and Florida. For example, seagrasses have declined in many areas of the IRL (Virnstein

and Morris 1996). Seagrass loss and environmental degradation of submerged lands

continue despite the existing federal and state regulatory programs. Examples of

regulatory programs that should positively affect seagrasses include Florida Department

of Environmental Protection (FDEP) and U.S. Army Corps of Engineers (COE) dock

construction, Environmental Resource Permitting (ERP), and Environmental Protection

Agency (EPA)/FDEP water quality standards (light attenuation through turbidity set for

phytoplankton). However, state and federal regulatory programs have not totally stopped

the loss of seagrasses and the degradation of submerged lands. A steady increase in 

coastal populations has greatly increased Florida’s assignment of enforcement

responsibilities, including responsibilities for enforcing environmental and boating

regulations, without a proportional increase in staff for the Florida Marine Patrol.

Stormwater management systems have been or are being installed; however, the Florida

IRL Act of 1990 covers only waste water treatment plants and does not cover other large

inputs that will affect water quality, which in turn could affect seagrasses (e.g., industrial

discharges, brine disposal, canals, processing plants).

Many seagrass ecosystems are known to recover very slowly even under the most

natural, pristine conditions. Although transplantation has had limited success, previous
1.7-5

mitigation efforts for loss of seagrass beds have failed (Fonseca et al. 1998). Until

recently, Halophila species have not been transplanted successfully in the field and

studies underway are incomplete (Heidelbaugh et al. 1999). Current efforts are

insufficient to protect critical seagrasses. This was also the conclusion and

recommendation of scientists attending the International Seagrass Workshop in

Kominato, Japan in August 1993. Kenworthy and Haunert (1991) concluded that the

State of Florida’s light and turbidity standards were inadequate to protect seagrasses. See

“State Conservation Measures; Surface Water Quality Standards” for a description of

these standards under the Florida Administrative Code (F.A.C.), Chapter 62-302.
1.8-1

1.8 Listing Determination

Based on available information, NMFS concluded that Johnson’s seagrass warrants

listing as a threatened species. This species is rare, has a limited reproductive capacity,

and is vulnerable to a number of anthropogenic and natural disturbances. Also, it

exhibits the most limited geographic distribution of any seagrass. Within its small

geographic range (lagoons on the east coast of Florida from Sebastian Inlet to central

Biscayne Bay), it is one of the least abundant species. Because of its limited

reproductive capacity and energy storage capacity, it is less likely to survive

environmental perturbations and to be able to repopulate an area when lost. Finally,

environmental degradation and habitat loss have continued despite existing federal and

state conservation efforts. 

H. johnsonii was listed as threatened on September 14, 1998 (63 FR 49035)(Appendix I). 

Critical habitat for Johnson's seagrass was designated on April 5, 2000 (65 FR 17786)

(Appendix II).
1.9-1

1.9 Conservation Measures

1.9.1 Federal Conservation Measures

NATIONAL MARINE FISHERIES SERVICE (NMFS)

Johnson’s seagrass is directly protected by provisions of the ESA under NMFS

jurisdiction. Federal agencies conducting, permitting, or funding actions that may affect

Johnson’s seagrass are required to consult with NMFS Protected Resources Division.

While the provisions of the ESA may have reduced certain threats, the adverse affects of

some of these actions continue.

Federal agency actions or programs that may affect Johnson’s seagrass include: COE

authorization of projects affecting waters of the United States under section 404 of the

Clean Water Act and Section 10 of the Rivers and Harbors Act (i.e., beach

renourishment, dredging, filling, and related activities including the construction of docks

and marinas); EPA authorization of pollutant discharges and management of freshwater

discharges into waterways and state directives to develop numerical nutrient criteria by

2003; U.S. Coast Guard (USCG) regulation of vessel traffic; management of national

refuges and protected species by USFWS; management of vessel traffic and other

activities by the U.S. Navy; authorization of state coastal zone management plans by

NOAA/NOS; and management of commercial fishing and protected species by NMFS

(NMFS 1998, page 49041). 
1.9-2

The NMFS Habitat Conservation Division (HCD) acts in an advisory capacity in the

protection of natural resources under NMFS purview and coordinates with the COE and

other federal agencies on any federal projects which may affect these resources. Federal

agencies, including NMFS/HCD, support the Living Marine Resource mandates,

Submerged Aquatic Vegetation (SAV) policy (adopted May 1997), and Essential Fish

Habitat (EFH) amendments of the South Atlantic Fishery Management Council

(SAFMC) and the Atlantic States Marine Fisheries Commission (ASMFC).

SOUTH ATLANTIC FISHERY MANAGEMENT COUNCIL (SAFMC)

The SAFMC plays an advisory role in the protection of habitat essential to managed

species as directed by the Magnuson-Stevens Fishery Conservation and Management

Act. The SAFMC and NMFS have coordinated their efforts to address their respective

mandates in the Act. The SAFMC actively comments and makes recommendations to

federal and state agencies that may affect EFH, including SAV. Under the new EFH

mandates of 1997, the SAFMC began identifying and describing EFHs and amending

existing fishery management plans to include these EFHs. The SAFMC has also

established a Habitat Advisory Panel and initiated workshops on habitat types, including

seagrass habitats.

ATLANTIC STATES MARINE FISHERIES COMMISSION (ASMFC)

Based upon the importance and need to protect SAV habitats for ASMFC managed

species, the ASMFC has developed policies in SAV and Habitat Conservation (ASFMC
1.9-3

1997). These policies have been incorporated into fishery management plans through

amendments that describe EFHs for ASFMC trust resources and emphasize the need to

protect and conserve SAV systems. The ASMFC encourages NMFS and USFWS to

adopt and implement the plans, policies, and amendments. Depending upon the level of

implementation, Johnson’s seagrass and its habitat may be indirectly protected by these

policies.

NATIONAL ESTUARY PROGRAM - INDIAN RIVER LAGOON NATIONAL

ESTUARY PROGRAM (IRLNEP)

The Federal Water Quality Act of 1987 recognized the poor health of the nation’s

estuaries and need for their protection, and stated a national interest in maintaining the

ecological integrity of the nation’s estuaries. Section 320 of the Water Quality Act

initiated the National Estuary Program.

The Indian River Lagoon Comprehensive Conservation and Management Plan

(IRLCCMP) was published by the IRLNEP in November 1996 and is sponsored by the

SJRWMD and the South Florida Water Management District (SFWMD) in cooperation

with the EPA. Priority problems identified in the IRLCCMP include loss of seagrass

beds and increasing stress on remaining beds, undesirable salinity fluctuations, and

increased nutrient loading. Action plans of the IRLCCMP include water and sediment

quality improvement, seagrass restoration and management, and endangered and

threatened species. The elements and action plans of the IRLCCMP are mutually
1.9-4

supportive and complement the management efforts of the State of Florida SWIM

program.

U.S. FISH AND WILDLIFE SERVICE (USFWS)

Seagrass habitat, including Johnson’s seagrass, is directly protected under the ESA by the

USFWS as a critical habitat for the endangered Florida manatee. Protective mechanisms

include section 7 consultations for dredging or water-dependent construction (including

docks and marinas), motorboat access and speed limits in seagrass beds to reduce prop

scarring, a long-term habitat monitoring program, the designation of manatee refuges and

sanctuaries (including the Virginia Key No Entry Zone in Dade County authorized under

62N-22 F.A.C.), and new efforts to assess and propose new manatee protection areas

(U.S. Fish and Wildlife Service 2000).

1.9.2 State of Florida Conservation Measures

ENVIRONMENTAL RESOURCE PERMIT (ERP) PROGRAM

The ERP program regulates dredging, filling, and other construction activities in

wetlands or other surface waters, activities in uplands that affect flooding, and all

stormwater management activities throughout the state (except within the limits of the

Northwest Florida Water Management District). The ERP program is designed to ensure

that alterations of uplands, wetlands, or surface waters do not degrade water quality,

cause flooding, or diminish habitat quality or quantity. ERP was adopted in 1994 under

Part IV, Chapter 373 of the Florida Statutes (F.S.), and is implemented cooperatively by
1.9-5

the FDEP and the state’s water management districts (WMDs). The SJRWMD and

SFWMD cooperate with the Central and Southeast FDEP District offices in the region

where H. johnsonii occurs. To allow an applicant to deal with only one agency when

seeking an ERP, the review and approval or denial of the permit is performed by either

FDEP or one of the WMDs, depending upon the type of activity involved. Operating

agreements signed by the agencies specify the division of permitting responsibilities

between the agencies. Rules implementing the ERP program have been adopted by both

FDEP (including Chapters 62-4, 62-113, 62-302, 62-312, 62-330, 62-340, 62-341, 62-

342, 62-343, 62-344, 62-B-49, 18-14, 18-20, 18-21 of the F.A.C.) and the WMDs

(including Chapters 40C-1, 0C-4, 40C-8, 40C-40, 40C-41, and 40C-400, F.A.C for the

SJRWMD, and Chapters 40E-1, 40E-4, 40E-40, 40E-41, F.A.C. for the SFWMD). 

The ERP program replaced two separate permitting programs, the Wetland Resource

Permit program (WR) and the Management and Storage of Surface Waters program

(MSSW). The WR program controlled dredge and fill activities, and was implemented

exclusively by the Department of Environmental Regulation (now FDEP), while the

MSSW program managed activities affecting stormwater and flooding, and was

implemented exclusively by the five WMDs. Legislation establishing the ERP program

included several grandfathering provisions that retain the above WR and MSSW

permitting programs for certain activities listed in subsections 373.414(11)-(16), F.S. For

these grandfathered activities, Chapter 62-312 F.A.C. and the MSSW permitting rules

adopted under Part IV, Chapter 373, F.S. remain in effect as they existed prior to October
1.9-6

3, 1993. FDEP and the WMDs implement the programs covering these grandfathered

activities in accordance with the same division of permitting responsibilities that governs

the ERP program.

Proprietary Authorization to Conduct Activities on Sovereign Submerged Lands

In addition to regulatory permission, activities on sovereign (state-owned) submerged

lands also require what is termed “proprietary authorization”. Statutory authority for

proprietary authorization is provided by Chapter 253, F.S., and the rules implementing

this statute are in Chapter 18-21, F.A.C. Requests for proprietary authorization are

reviewed in conjunction with the regulatory application and are granted or denied at the

same time. More stringent resource protection measures are afforded for the state's

Aquatic Preserves designated under Chapter 258, F.S. Additional requirements for

Aquatic Preserves include: more restrictive water quality requirements (62-4.244(2),

F.A.C.) and adequate demonstration that the activity is clearly within the public interest

based on the public interest criteria listed in Chapter 373.414(1)(a), F.S. The majority of

H. johnsonii habitat is already located within existing Aquatic Preserves and Outstanding

Florida Waters (OFWs) (See Aquatic Preserves and OFWs Sections).

Joint Coastal Permits

Chapter 161, F.S. provided the FDEP Bureau of Beaches and Coastal Systems with the

authority to regulate coastal construction activities via a Coastal Construction Permit

(CCP). However, a Joint Coastal Permit (JCP) is issued when both a CCP (pursuant to
1.9-7

Section 161.041, F.S.) and an ERP permit (pursuant to Part IV, Chapter 373, F.S) are

required. Chapter 62B-49, F.A.C. outlines the procedures and requirements that must be

met to obtain a JCP. Requests for proprietary authorization are reviewed in conjunction

with the JCP application and are granted or denied at the same time.

The COE and FDEP/WMDs have joint WR and ERP permit application forms. FDEP or

one of the WMDs acts as the lead agency to receive all applications for state and federal

wetland permits and forwards copies of such applications to the COE within five working

days. Issuance of the state permit constitutes federal section 401 water quality

certification, unless such certification is specifically waived in the permit. However, the

actual state and federal permitting processes remain separate, and applicants are required

to obtain all required federal, state, regional, and local permits prior to initiating

construction activities.

Delegation of ERP to Local Governments

To further streamline the permitting process, Section 373.441, F.S. provides authority for

FDEP and the WMDs to delegate all or a portion of ERP to local governments. If

granted delegation for specified activities, all necessary authorizations under the ERP

program as well as any needed additional local permits will be granted or denied at the

same time by the local government. To implement this statutory authority, FDEP has

adopted a rule (Chapter 62-344, F.A.C.) specifying the application procedures and

outlining criteria that will be used to approve or deny a delegation request. At present
1.9-8

there has been no full delegation of ERP to any local government, although a

comprehensive delegation to Broward County is currently nearing finalization. A partial

delegation of a Noticed General Permit for single family home construction within the

Indian Trails Water Control District has been granted to Palm Beach County. A full

delegation of the stormwater permitting program (under Chapter 62-25, F.A.C.) has been

granted to the City of Tallahassee in northwest Florida.

FDEP AQUATIC PRESERVES PROGRAM

The FDEP Aquatic Preserves program (adopted under Chapter 258, F.S.) provides

additional water quality protection to sovereign submerged lands with exceptional

biological, aesthetic, or scientific value. Five of the state's 43 aquatic preserves are

located within the region where H. johnsonii occurs. Rules implementing the Aquatic

Preserves program are Chapter 18-18, F.A.C., which is specific to the Biscayne Bay

Aquatic Preserve and Chapter 18-20, F.A.C., which covers all other aquatic preserves. 

Special management plans have been developed for all aquatic preserves.

Aquatic Preserves within the range of H. johnsonii:

• Indian River Lagoon, Malabar to Sebastian (Brevard/Indian River Counties)

• Indian River Lagoon, Vero Beach to Ft. Pierce (Indian River/St. Lucie Counties)

• Indian River Lagoon, Jensen Beach to Jupiter Inlet (St. Lucie/Martin/Palm Beach

Counties)
1.9-9

• Loxahatchee River to Lake Worth Creek (Martin/Palm Beach Counties)

• Biscayne Bay (Dade County)

SURFACE WATER QUALITY STANDARDS; CLASSIFIED WATERS

The FDEP’s surface water quality standards, adopted in 1979, are designed to protect the

public health or welfare and to enhance the quality of waters of the State. The State’s

surface waters have been separated into five classes according to their designated uses

(F.A.C. 62-302). These water quality classifications are arranged in order of the degree

of protection required, with Class I water having generally the most stringent water

quality criteria and Class V the least. Classifications are as follow: Class I - Potable

Water Supplies; Class II - Shellfish Propagation or Harvesting; Class III - Recreation,

Propagation and Maintenance of a Healthy, Well-Balanced Population of Fish and

Wildlife; Class IV - Agricultural Water Supplies; and Class V - Navigation, Utility and

Industrial Use. The majority of Florida’s surface waters are designated Class III waters. 

The range of Johnson’s seagrass occurs predominantly within Class III waters and in a

few locations designated as Class II water. 

Class I, II and III waters share water quality criteria established to protect “recreation and

the propagation and maintenance of a healthy, well-balanced population of fish and

wildlife.” The nutrient, light and turbidity standards for Class I-III waters are: 

a) Nutrients: A narrative criterion which states, “In no case shall nutrient concentrations

of a body of water be altered so as to cause an imbalance in natural populations of
1.9-10

aquatic flora or fauna.”; b) Transparency (light): The depth of the compensation point

for photosynthetic activity shall not be reduced by more than 10% as compared to the

natural background value; and c) Turbidity: < 29 Nephelometric Turbidity Units above

natural background conditions (F.A.C. 62-302.48 (b); 62-302.68; and 62-302.70).

Water-quality based targets are to be developed by FDEP and WMDs for use in

protecting seagrass populations threatened by eutrophication (D. Joyner pers. comm.

2000). The WMDs will be establishing Pollutant Load Reduction Goals (PLRGs) for

SWIM waters. The developed PLRGs will be used by the FDEP as a basis for

establishing Total Maximum Daily Loads (TMDLs) for waters on the State of Florida’s

(303(d)) list of impaired waters (expected completion date of 2012). The agencies will

use these numerical nutrient criteria to identify needed management activities as part of

the state’s SWIM plans and other water management plans.

OUTSTANDING FLORIDA WATERS (OFW)

A water body may be designated as an OFW as well as being classified as Class I, II or

III. More than 200 water bodies throughout the state have been designated as OFWs,

where more stringent water quality and permitting standards apply. These include the

aquatic preserves previously discussed, as well as waters within national and state parks.

Chapter 62-302.700 lists those waters designated as OFWs. In addition to the aquatic

preserves previously listed, the major OFWs in the range of Johnson's seagrass include:

Archie Carr, Hobe Sound and Loxahatchee National Wildlife Refuges; Savannas State
1.9-11

Reserve; John D. MacArthur State Park; and Sebastian Inlet, Ft. Pierce Inlet, Hugh

Taylor Birch, John U. Lloyd Beach, and Oleta River State Recreation Areas (F.A.C. 62-

302.700).

FDEP BUREAU OF INVASIVE PLANT MANAGEMENT

The FDEP Bureau of Invasive Plant Management regulates the importation, possession,

collection, planting, relocation, or treatment of aquatic plants pursuant to Chapter 369,

F.S. (implemented by Chapters 62C-20, 62C-52 and 62C-54, F.A.C.). The Bureau is

charged with protecting sovereign lands from improper and excessive collection of native

aquatic plants for purposes of sale, revegetation, restoration, or mitigation.

FDEP ECOSYSTEM MANAGEMENT INITIATIVE

FDEP began the Ecosystem Management Initiative in 1993. Ecosystem management

provides for new, voluntary, parallel permitting and approval processes that give

regulatory incentives to applicants. These optional processes require that projects be

designed to provide some net environmental benefit. All of these optional processes are

alternatives to, but do not replace, the current permitting system.

FLORIDA FISH AND WILDLIFE CONSERVATION COMMISSION (FWC)

Division of Marine Resources

The FWC actively maintains a permitting program within its Division of Marine 
1.9-12

Fisheries to address the harvest of seagrass for educational, scientific and restoration

purposes. Fishery practices that may harm seagrass in state waters are also regulated by

the FWC, aside from Aquaculture which is regulated by the Florida Department of

Agriculture and Consumer Services (FDACS). The FWC, Bureau of Protected Species

Management acts as a commenting agency contributing to the protection of seagrass

through the ERP programs administered by the FDEP and WMDs. Comments are

provided based on the protection of manatee and marine turtle habitat, which includes

Johnson’s seagrass throughout its range. The FWC is largely responsible for the

enforcement of state regulations regarding seagrass and marine habitat protection through

the Division of Law Enforcement’s Bureau of Marine Enforcement. Managementoriented research programs for seagrass are a significant part of the FWC’s FMRI

operations. Seagrass outreach and education efforts are an integral part of the operation

of the Division of Marine Fisheries, Office of Environmental Services, and FMRI.

FLORIDA DEPARTMENT OF AGRICULTURE AND CONSUMER SERVICES

(FDACS)

Florida Regulated Plant Index

The Florida Regulated Plant Index (established pursuant to Section 581.185, F.S.) is

administered and maintained by the FDACS Division of Plant Industry via Chapter 5B40, F.A.C. Listed plant species are categorized as endangered, threatened, or

commercially exploited. Permits for the taking, transport, and sale of plants on the

Regulated Plant Index are reviewed by FDACS, but there is no provision for FDACS to
1.9-13

regulate construction or other land alteration activities. Halophila johnsonii was listed as

a state endangered species but then subsequently removed from the Regulated Plant

Index a few years prior to receiving federal listing. Although Section 581.185, F.S.

provides for the automatic listing as a state endangered species of “all species determined

to be endangered or threatened pursuant to the federal ESA of 1973,” Johnson’s seagrass,

since its Federal listing in 1998, has not been placed back on the Regulated Plant Index.

Florida Endangered Plant Advisory Council

FDACS’s Division of Plant Industry acts as liaison for the Endangered Plant Advisory

Council (established under Section 581.186, F.S.) which serves to improve the protection

of threatened, endangered, and commercially exploited plant species on the Regulated

Plant Index. The council periodically examines listed species, as well as other native

plants that have been proposed for inclusion on the Regulated Plant Index, to determine

whether a particular plant species should be removed from the list, transferred to a

different category, or added to the list.

Division of Agricultural Environmental Services

FDACS Division of Agricultural Environmental Services regulates pesticide use within

the state (via Chapter 487, F.S., and Chapter 5E, F.A.C.), and is responsible for

coordinating state strategies to protect federally-listed threatened and endangered species

from the use of pesticides.
1.9-14

LAND CONSERVATION ACT OF 1972

The Land Conservation Act of 1972 (Chapter 259, F.S.) establishes a land acquisition

program to conserve and protect environmentally endangered lands in Florida. Criteria

for selecting lands include consideration of important wildlife and plant habitats,

including endangered and threatened species habitats.

FLORIDA FOREVER ACT

The Florida Forever Act (FFA) (Chapter 259, F.S.), passed by the 1999 Florida

Legislature, was effective as of July 2000. This act replaces the Florida Preservation

2000 Act which created a funding mechanism to support land acquisition programs in

Florida and was implemented by Chapter 18-8, F.A.C., Conservation and Recreation

Lands (CARL). Changes to this legislation are expected relative to the operation of the

FFA. Federal listing of H. johnsonii may encourage land acquisition or other land

conservation measures by the state.

THE FLORIDA ENVIRONMENTAL LAND AND WATER MANAGEMENT ACT OF

1972

The Florida Environmental Land and Water Management Act of 1972 (Sections 380.10-

12, F.S.) created the Area of Critical State Concern Program, which establishes a

procedure for increased protection of lands of statewide importance, including critical

habitat for threatened or endangered species. This act also establishes the Development

of Regional Impact program, which requires that permit applications for certain large-
1.9-15

scale developments affecting more than one county must undergo more stringent review,

including review of the development’s impact on wildlife habitat.

STATE COMPREHENSIVE PLAN

The State Comprehensive Plan (Chapter 187, F.S.) includes goals and policies to

conserve wildlife habitat and prohibit the destruction of endangered species and

associated habitat. Local government comprehensive plans must be consistent with

provisions in the state plan. Listing of H. johnsonii may encourage its conservation

through Florida's planning procedures, supervised by the Florida Department of

Community Affairs.

FLORIDA NATURAL AREAS INVENTORY

The Florida Natural Areas Inventory (FNAI) was established in 1981 as a cooperative

effort of FDEP and the Nature Conservancy. Funding for FNAI has been provided

primarily by the CARL Trust Fund (authorized by Section 253.023, F.S.). One of the

primary tasks of FNAI is to collect and disseminate information on the status and

distribution of threatened and endangered species of plants and animals in Florida. These

data facilitate environmentally sound planning and natural resource management. FNAI

supported the listing of H. johnsonii.

ST. JOHNS RIVER AND SOUTH FLORIDA WATER MANAGEMENT DISTRICTS

Indian River Lagoon Surface Water Improvement and Management Plan (IRL SWIM)
1.9-16

and Indian River Lagoon National Estuary Program Comprehensive Conservation and

Management Plan (IRLCCMP)

These plans list seagrass as the most critical habitat in the IRL, and have been developed

with the goal of restoring the integrity and functionality of seagrass beds within this

system (Steward et al. 1994, IRLNEP 1996).

1.9.3 Summary of Conservation Measures

A variety of conservation measures exist to protect H. johnsonii and its habitat. H.

johnsonii habitat is included in the designation of critical habitat for the Florida manatee

and is therefore subject to ESA section 7 consultation. H. johnsonii habitat is also

protected through Aquatic Preserves or designated OFWs. However, these conservation

measures must be further analyzed to determine if they will ensure the long term

protection of the species or the maintenance of its geographic distribution. 
2.0-1

2.0 RECOVERY STRATEGY

The recovery strategy for H. johnsonii is based on two key premises: 1) very little

information is known about the species, including its reproductive biology, historical

distribution, or methods for restoration, and 2) it is not certain if existing regulatory

mechanisms are adequate to protect the species. Based on this information the recovery

program was developed to: 1) conduct monitoring and research to better define habitat

requirements, life history and restoration techniques; and 2) protect the species in its

current state through ESA consultation, assessment of the adequacy of existing

regulatory mechanisms, and outreach.
2

 Self-sustaining population is a population that has been documented to persist for at least 10

years. 

3.0-1

3.0 RECOVERY OF JOHNSON’S SEAGRASS

3.1 Objectives and Criteria

The recovery objective for H. johnsonii is to delist the species by assuring its long-term

persistence throughout its range. Halophila johnsonii should be considered for delisting

when all of the following criteria are met:

(1) The species’ present geographic range remains stable for at least 10 years or

increases,

(2) Self-sustaining populations2 are present throughout the range at distances less

than or equal to the maximum dispersal distance to allow for stable vegetative

recruitment and genetic diversity, and

(3) Populations and supporting habitat in its geographic range have long-term

protection (through regulatory action or purchase acquisition). 

Quantitative information, including the number of self-sustaining populations necessary

and the quality and quantity of habitat required to further define and meet these criteria,

are included as recovery plan actions in Section C below.

3.1.1 Revision of Recovery Criteria

The recovery criteria, and boundaries and locations of critical habitats, may be revised on

the basis of new information. A long-term research and management plan will be
3.0-2

developed by a Johnson’s Seagrass Implementation Team. The team core group will be

members of the Recovery Plan Team and will use the approved Recovery Plan in

addressing and implementing recovery strategies for H. johnsonii.
3.2-1

3.2 Recovery Program

The recovery actions for H. johnsonii have been organized under eight major recovery

needs (or actions): 1) Identify and protect populations and habitat; 2) Initiate a rangewide monitoring program; 3) Refine habitat requirements of H. johnsonii; 4) Conduct

detailed life history studies of H. johnsonii to examine vegetative fragment dispersal,

survival, and sexual reproduction; 5) Determine and implement habitat management

needs and techniques; 6) Identify the genetic diversity and genetic structure of H.

johnsonii across its geographic range; 7) Develop restoration techniques; and 8)

Formulate an educational outreach program to increase awareness of H. johnsonii and its

status. Each of the major actions includes an introductory narrative followed by specific

recovery actions for the species. Unless otherwise specified, actions described apply to

the entire range of the species. 

Action 1. Identify and protect populations and habitat

Existing populations of H. johnsonii must be protected from present and foreseeable

threats, including those that involve direct removal of the plant and/or adverse

modification of its habitat. Protective management measures should be applied to entire

habitats supporting Johnson’s seagrass. Ten areas in the geographic range of Johnson's

seagrass were designated as critical habitat (65 FR 17768) (Appendix II). This

designated area accounts for approximately 22,574 acres or 9,139 hectares. 
3.2-2

A long-term management program should be established based on special protection

areas (areas having suitable habitat characteristics for supporting Johnson’s seagrass).

Elements such as state lands, aquatic preserves, acquisition, conservation agreements,

easements, donations, or sanctuary arrangements will also be used for the protection of

Johnson’s seagrass populations and habitat.

1.01. Develop detailed baseline distribution maps (In coordination with Section 2,

Monitoring).

1.01.A. Identify areas with persistent populations.

1.01.B. Map and delineate areas with flowering populations.

1.01.C. Identify areas of high abundance or areas that are conducive to the 

survival of the species. 

1.02. Protect the geographic extremes of the range and genetically unique populations

(In coordination with Section 5, Management and Section 6, Genetics).

Action 2. Initiate a range-wide monitoring program.

Factors affecting the recruitment, survival, and spread of a rare plant are complex

(Schemske et al. 1994). For many seagrasses, little is known about their reproductive

ecology, especially the production and dispersal of sexual or asexual propagules, two

processes which are critical for their persistence or recovery. The patchiness and limited

geographic range of H. johnsonii beds presents challenges and opportunities in
3.2-3

monitoring the status of this rare species. Monitoring should provide information on the

recruitment and mortality of patches as well as providing information on inter- and intrapatch dynamics. Because of the extremely limited latitudinal range of H. johnsonii,

monitoring should detect any changes in the northern or southern distributional limits or

range extensions of this species, i.e., intensive surveys should be undertaken to precisely

determine these distributional boundaries and to especially assess their year-to-year

stability. To satisfy the criteria for de-listing, there is also a critical need to determine

whether population stability is affected by patch size and spacing and whether this varies

from north to south. Distribution maps have important implications regarding the

stability of this rare species and its ability to recover from stochastic perturbations that

may eliminate individual patches or entire populations. An important goal of the initial

mapping would be to identify if any major distributional gaps presently exist in the

southern part of the range. 

Random sampling strategies, unless highly intense, are inappropriate for assessing the

recovery potential for H. johnsonii because they could misrepresent the distribution and

abundance of this species by having a relatively high probability for sample points to

miss patches/beds. Rather, by surveying selected areas to locate H. johnsonii patches and

establishing sampling stations both within and outside of patches, much information

regarding patch dynamics can be gained. Because of H. johnsonii's small size and

understory growth habit, and also its deep-edge growth habit and resolution limitations,

aerial photography cannot be used to monitor changes in its distribution and abundance.
3.2-4

Initial aerial photography surveys of the region from Jupiter Inlet south, however, would

be useful for locating potential seagrass-occurrence sites for subsequent ground-truthing

surveys. The FWC Bureau of Protected Species Management's 1999 dock study and 

1996-1997 marina siting survey (Smith and Mezich 1999, Bureau of Protected Species

Management 2000), and Palm Beach County Department of Environmental Resource

Management (DERM) data (Palm Beach County DERM 1992, 1990) would also be

useful for locating potential seagrass-occurrence sites. Spatially explicit, in-situ

monitoring would then be required to verify distribution and abundance. The shoot

density and cover within a statistically representative number of patches could be

determined and tracked along with the variability of patch location and size (determined

by Differential Global Positioning System (DGPS)) and the collection of a suite of

environmental parameters thought to affect these characteristics (such as optical water

quality, water depth, and salinity). This combined tracking of information would allow

correlative examination of the role of year-to-year environmental variation in affecting

the vigor and abundance of this species. Monitoring should attempt to match up study

sites with locations where current and past water quality data exist.

The relative contributions of vegetative growth and propagule dispersal versus sexual

reproduction and seed recruitment (unknown for this species) on the maintenance,

establishment, and genetic diversity of patches, need to be understood for effective

conservation and management (Schemske et al. 1994). The presence of numerous small

patches across the marine landscape provides for an increased chance that some patches
3.2-5

will survive perturbations and provide a recruitment source for post-impact recovery. 

Recent work on seagrass population genetics has demonstrated the importance of

sampling over several spatial scales to determine the relative importance of various 

reproductive strategies to population establishment and maintenance, demography, and

genetic diversity (Procaccini et al. 1996). This information is critical to resource

managers in their evaluation of species recovery in the context of demonstrated spatial

and year-to-year patterns of population distribution and abundance. Primary goals of a

monitoring program are an understanding of H. johnsonii’s demography and the

determination of whether the density, abundance, and distribution of beds are expanding

or declining.

2.01. Determine whether the distribution and size of beds are expanding or declining and

identify factors influencing expansion or decline.

2.02. Determine the precise northern and southern distributional limits of H. johnsonii

and monitor the temporal variation in these limits using DGPS and in-situ sampling.

2.03. Determine whether patch size, abundance, or spacing vary from north to south, and

identify if there are presently any large distribution gaps (see Protect Populations and

Habitat section).
3.2-6

2.04. Monitor persistence. Establish permanent monitoring plots at (a) the northern and

southern distribution limits, (b) the geographic extremes of the natural lagoon systems

within the known geographic range (i.e., the southern end of the IRL and the northern

end of Lake Worth), (c) sites with existing or long-term water quality data, and (d) sites 

identified to have unique or diverse genotypes present (e.g., Boynton Beach, Boca Raton,

etc.). Annual monitoring should be conducted for 10 years to determine whether criteria

for de-listing have been met. 

Action 3. Refine habitat requirements of Halophila johnsonii.

With no sexual reproduction, limited dispersal capability, and limited capacity to store

energy and nutrients during periods of stress, H. johnsonii must sustain continuous

vegetative growth and reproduction in order to replace natural mortality. Therefore,

favorable environmental conditions must be nearly continuously maintained for

continuous growth. Critical environmental factors to support seagrasses include, but are

not restricted to, light, temperature, salinity, and unconsolidated sediments. Where H.

johnsonii grows, conditions usually include light levels maintained at a minimum of 10%

surface incident light, salinity of at least 15 ppt, water temperature between 10o C and 35o

C, and sediments that are unconsolidated sand or sand mixed with silt-clay. The effects

of short-term poor conditions (i.e., low light or poor water quality) on H. johnsonii are

currently unknown.
3.2-7

3.01. Identify sites with and without H. johnsonii. At these sites, conduct a

correspondence analysis between H. johnsonii distribution/abundance and environmental

factors (habitat characteristics) including: temperature, salinity, light intensity, water

motion, tidal exposure, sediment characteristics and stability, and eutrophication (Also

see Actions 7.01, 7.02 and 7.03).

3.02. Locate ephemeral populations of H. johnsonii and identify the characteristics

(listed in Action 3.01) of these sites.

3.03. Identify the habitat characteristics which favor populations with female flowers

(assuming male flowers should co-occur with females) and experimentally manipulate

these conditions in the laboratory or mesocosm to attempt to induce flowering.

3.04. Conduct experiments to determine the effect of other seagrass species on the

distribution and abundance of H. johnsonii and assess the similarity of habitat

requirements between H. johnsonii and other species.

3.05. Determine if water quality and water management programs are appropriate for

determining changes in conditions which would affect the continuous vegetative growth

and reproduction of H. johnsonii.
3.2-8

3.06. Select areas throughout the geographic range of the species which have suitable

environmental conditions for perennial and flowering populations for use in the

development and management of special protection areas for H. johnsonii (In

coordination with Action 5.13). 

Action 4. Conduct detailed life history studies of Halophila johnsonii to examine

vegetative 

fragment dispersal, survival, and sexual reproduction. 

Initial field and mesocosm research and surveys of natural populations indicate that

female flowers are formed in isolated populations, but there is still no report of the

presence of male flowers. Male flowers are either non-existent or very rare, and asexual

reproduction could be the primary means of growth and dispersal of this species. Yet

there is evidence for a wide range of fluctuation in populations, and considerable efforts

are needed to explain and understand the recovery and colonization processes. Dispersal

and recruitment by vegetative fragments is presumed to be an important mechanism for

maintaining the disjunct populations of H. johnsonii. Research efforts should focus on

determining the maximum dispersal distances by vegetative fragments, and the critical

life stages which are responsible for maintaining populations. Experimental design

should cover the following: 

4.01. Estimate rates of new short shoot (the vertical shoot formed by the branching of

the horizontal rhizome/apical meristem) formation and death rates in natural populations
3.2-9

and in experimental fragments manipulated in mesocosms under different environmental

conditions.

4.02. Experimentally determine the mechanism for recruitment of patches (clones), and

maximum dispersal distances of vegetative fragments. Use this information to determine

the number of self-sustaining populations necessary to ensure their presence throughout

the range.

4.03. Experimentally manipulate in the laboratory or mesocosm, light, temperature,

salinity, and nutrients to determine their effects on flowering and growth of vegetative

fragments. 

4.04. Collect and transplant fruits of H. johnsonii to determine whether fruits of H.

johnsonii germinate and whether apomixis occurs.

Action 5. Determine and implement habitat management needs and techniques.

Maintenance of suitable habitat for this species will require use of management

procedures to alleviate or prevent degrading conditions (based on habitat requirements).

Section 7(a)(2) of the ESA requires every federal agency to insure that any action it

authorizes, funds, or carries out is not likely to jeopardize the continued existence of any

listed species or result in the destruction or adverse modification of critical habitat (50

CFR 402.01). The feasibility of developing a 4(d) rule with specific protective
3.2-10

regulations for H. johnsonii, such as extending take prohibitions to this threatened plant,

will be examined. Water quality-based targets are to be developed by the FDEP and

WMDs for use in protecting seagrass populations threatened by eutrophication (D. Joyner

pers. comm. 2000). The WMDs will develop PLRGs for SWIM waters, and the FDEP

will use these values as a basis for determining TMDLs for waters on the State of

Florida’s 303(d) list of impaired waters. The agencies will use these PLRGs and TMDLs

to identify needed management activities as part of the state’s SWIM plans and other

water management plans. 

Successful management of Johnson’s seagrass and its habitat will require an

improvement in the accuracy of impact assessment on the species and its habitat and an

examination of the interagency review process for projects that may impact the species

and its habitat. Identifying impacts to seagrass habitat, particularly from large projects,

is, in the long run, more important than a "point-in-time" management approach of

avoiding currently existing patches. Seagrasses are provided a greater level of protection

from human activities on those state-owned submerged lands within designated aquatic

preserves and within the boundaries of federally-designated areas. Existing regulatory

authorities and seagrass protection regulations will be examined and applied to protect H.

johnsonii and its habitat. A multi-agency management approach, utilizing various

educational and enforcement methods, will be implemented to reduce prop scarring and

trampling of shallow water seagrass beds. Over the long term, this comprehensive
3.2-11

approach should reduce scarring or trampling to levels that do not significantly affect

habitat quality and quantity.

5.01. Establish and convene an Implementation Team to develop a long-term research

plan for the species and coordinate implementation of recovery plan actions. 

5.02. Recommend to Federal and state agencies that they adopt sampling protocols for

H. johnsonii for the permit application and monitoring requirements of project sites (see

Appendix III).

5.03. Incorporate pre- and post-construction (of in- and over-water structures)

monitoring data of H. johnsonii distribution and abundance, from federal, state, and local

agencies, into a centralized Geographic Information System (GIS) tracking system to

improve protection and management and to determine cumulative impacts.

5.04. Provide educational opportunities and workshops for federal, state, and local

permitting agencies, including training in field identification, sampling protocols, and the

identification of designated critical habitat.

5.05. Establish federal and state interagency coordination during the permit review

process (e.g., NMFS, COE, FDEP, SJRWMD, SFWMD, FWC) for projects that may
3.2-12

affect H. johnsonii or its habitat so that impacts to the species can be avoided or

minimized.

5.06. Improve or maintain water quality and sediment conditions appropriate for

continuous vegetative growth and reproduction of natural populations of H. johnsonii

throughout its geographic range, addressing point and non-point sources and water

quality-based targets (PLRGs and TMDLs). Coordinate these actions with existing

programs, including, but not exclusively, the Indian River Lagoon National Estuary and

SWIM programs and the Lake Worth Management Plan.

5.07. Establish PLRGs and determine TMDLs for a specific water body or segment

within a water body, describing the management actions required to reach these

guidelines (including stormwater treatment, wastewater reuse, and best management

practices for upland use).

5.08. Monitor water bodies, or the segments within, for the predicted responses of water

quality and seagrass to the implementation of water quality management actions and

assess the effectiveness of these specific management actions.

5.09. Assess current federal, state, and local seagrass protection regulations and

programs (specifically those addressing human activities on submerged lands and within
3.2-13

the boundaries of federally-designated areas) for their level of effectiveness in protecting

H. johnsonii and its habitat.

5.10. Assess enforcement efforts of existing submerged lands/seagrass protection

regulations to determine their effectiveness in protecting H. johnsonii. Implement

modifications to increase effectiveness of enforcement actions, if needed. 

5.11. Preserve natural shoreline buffers on waterfront properties and encourage shoreline

restoration.

5.12. Identify and recommend the acquisition of privately-owned submerged land

vegetated with H. johnsonii and its adjacent uplands through local, regional, state and

federal programs. Public acquisition of these few tracts will preserve the seagrass habitat

associated with them and provide upland watershed buffer protection.

5.13. Implement a multi-agency approach management program to reduce prop scarring

and trampling of shallow water seagrass beds. The management program should use

methods including increased boater education, installation of channel markers, active

enforcement, and the establishment of limited motoring zones or closure areas. 
3.2-14

5.14. Determine whether specific protective regulations for H. johnsonii will be

developed under section 4(d) of the ESA in order to provide for the conservation of the

species.

5.15. Establish “adverse modification” and “jeopardy” guidelines for H. johnsonii for

use in section 7 consultation under the ESA.

Action 6. Identify the genetic diversity and genetic structure of Halophila johnsonii

across its geographic range.

 Genetic studies should continue to determine whether other pockets of higher genetic

diversity exist, especially at the southern extreme of this species’ range. These studies

should also look for genetic indicators of sexual reproduction and use more sophisticated

methods to identify the number of genetic individuals present in the species range. 

However, even if sexual reproduction or dispersal of fragments occurs, physical isolation

resulting from the disjunct distribution of this species may still pose a threat to its

persistence because of negative effects of inbreeding and clonal reproduction. Additional

studies should determine whether indices of genetic diversity are correlated with species

persistence. If the genetic composition of populations is linked to ecologically important

processes such as growth rate and survival, then these traits and genotypes can be

identified in specific populations and targeted for protection.
3.2-15

6.01. Determine the range of genetic variability and identify genetically unique

populations within the species' geographic range.

6.02. Determine whether indices of genetic diversity are correlated with species

persistence. 

Action 7. Develop restoration techniques.

Because of its apparent lack of sexual reproduction, inability to disperse by sexual

propagules, and its small and relatively fragile stature, H. johnsonii may have a limited

capacity for recovering from disturbance or total destruction (removal). The extant

populations are comprised mainly of non-contiguously distributed patches, which limits

the ability of the plant to recover from disturbance by vegetative encroachment from 

adjacent undisturbed populations. Natural recruitment and recovery of H. johnsonii

within localized populations may be substantial. However, because of the limited or

absent sexual reproduction in this species, the recovery of lost populations may be

enhanced by transplantation of natural or cultivated vegetative fragments.

7.01. Conduct mesocosm and field experiments to test the feasibility of transplanting

excavated and naturally-dislodged (free floating and intertidal driftline) vegetative

fragments of H. johnsonii under a broad range of environmental conditions.
3.2-16

7.02. Identify populations of H. johnsonii which grow and survive under different field

transplanting conditions.

7.03. Use reciprocal field and mesocosm transplants to test the effects of different water

depths, salinities, geographical ranges, and genetic stocks in controlling the distribution

and abundance of H. johnsonii. Identify key growth and demographic characteristics that

distinguish the source and the surviving transplant populations.

7.04. Develop a reliable methodology for transplanting H. johnsonii.

7.05. Use mesocosms to identify and maintain stocks of H. johnsonii that have superior

characteristics for restoration.

Action 8. Formulate an educational outreach program to increase awareness of

Johnson’s seagrass and its status.

Halophila johnsonii may have the most limited distribution of any seagrass on earth,

known to only occur in lagoons along 200 km of the southeast coast of Florida. It is the

first marine plant species to be listed under the ESA. Recovery objectives, based on its

threatened status are to: a) prevent the species from declining to an endangered status,

and b) delist the species based on the criteria stated at the beginning of this recovery

chapter. An educational outreach program will address the status of H. johnsonii, threats
3.2-17

to the species and its habitat, and management needs for protecting and conserving this

species.

Threats of destruction to H. johnsonii and its habitat include (1) dredging and filling, (2)

construction and shading of overwater structures, (3) prop scarring and anchor mooring,

(4) trampling, (5) altered water quality (such as stormwater runoff and turbidity), (6)

storms, and (7) siltation. Education outreach needs to address both anthropogenic and

natural threats and needs to be tailored to public citizens, fishers and boaters, and to

private and public agencies (including the COE, USCG, Federal Highway

Administration, Florida Department of Transportation) involved with projects or

activities that may affect H. johnsonii or its habitat.

The education efforts for H. johnsonii should assist in raising awareness for all seagrass

habitats, the valuable role that seagrass beds play in the marine environment, threats to

shallow coastal lagoon ecosystems (where human impacts are great), and the overall

decline of seagrass species despite existing protective regulations for submerged lands. It

will be important to integrate education about H. johnsonii into already existing

protection plans or education programs, such as the IRL National Estuary and SWIM

programs, State of Florida Coastal and Aquatic Managed Areas, and the Lake Worth

Management Plan.

8.01. Develop a Web Page for H. johnsonii and post updates on its recovery efforts.
3.2-18

8.02. Adapt existing education tools such as pamphlets and brochures on Florida

seagrasses to address H. johnsonii protection. 

8.03. Coordinate with federal, state, and local agencies, conservation groups, plant

societies, commercial and recreational boaters and fishers, SCUBA divers, and media to

develop a positive understanding of seagrasses and H. johnsonii.

8.04. Develop and evaluate educational materials and curricula with schools and local

environmental centers that introduce students to seagrasses, making sure to incorporate

information on H. johnsonii, its habitat, and the ESA.

8.05. Develop and present state/federal/Water Management District regulatory

workshops on survey protocol, effects of actions on H. johnsonii, and basic biology and

proper identification of the species.
3.2-19

3.2.1 Recovery Action Summary

The following is a summary list of Johnson’s seagrass recovery actions. Actions are

listed in the order that they appear in the Recovery Chapter and not in order of priority. 

1.01. Develop detailed baseline distribution maps (In coordination with Section

2, Monitoring).

1.01.A. Identify areas with persistent populations.

1.01.B. Map and delineate areas with flowering populations.

1.01.C. Identify areas of high abundance or areas that are conducive to 

the survival of the species. 

1.02. Protect the geographic extremes of the range and genetically unique

populations (In coordination with Section 5, Management; and Section 6,

Genetics).

2.01. Determine whether the distribution and size of beds are expanding or

declining and identify factors influencing expansion or decline. 

2.02. Determine the precise northern and southern distributional limits of H.

johnsonii and monitor the temporal variation in these limits using DGPS

and in-situ sampling. 

2.03. Determine whether patch size, abundance, or spacing vary from north to

south, and identify if there are presently any large distribution gaps (see

Protect Populations and Habitat section).

2.04. Monitor persistence. Establish permanent monitoring plots at (a) the

northern and southern distribution limits, (b) the geographic extremes of

the natural lagoon systems within the known geographic range (i.e., the

southern end of the IRL and the northern end of Lake Worth), (c) sites

with existing or long-term water quality data, and (d) sites identified to

have unique or diverse genotypes present (e.g., Boynton Beach, Boca

Raton, etc.). Annual monitoring should be conducted for 10 years to

determine whether criteria for de-listing have been met. 
3.2-20

3.01. Identify sites with and without H. johnsonii. At these sites, conduct a

correspondence analysis between H. johnsonii distribution/abundance and

environmental factors (habitat characteristics) including: temperature,

salinity, light intensity, water motion, tidal exposure, sediment

characteristics and stability, and eutrophication (Also see Actions 7.01,

7.02 and 7.03).

3.02. Locate ephemeral populations of H. johnsonii and identify the

characteristics (listed in Action 3.01) of these sites.

3.03. Identify the habitat characteristics which favor populations with female

flowers (assuming male flowers should co-occur with females) and

experimentally manipulate these conditions in either the laboratory or

mesocosm to attempt to induce flowering.

3.04. Conduct experiments to determine the effect of other seagrass species on

the distribution and abundance of H. johnsonii and assess the similarity of

habitat requirements between H. johnsonii and other species.

3.05. Determine if water quality and water management programs are

appropriate for determining changes in conditions which would affect the

continuous vegetative growth and reproduction of H. johnsonii.

3.06. Select areas throughout the geographic range of the species which have

suitable environmental conditions for perennial and flowering populations

for use in the development and management of special protection areas for

H. johnsonii (In coordination with Action 5.13).

4.01. Estimate rates of new short shoot (the vertical shoot formed by the

branching of the horizontal rhizome/apical meritstem) formation and

death rates in natural populations and in experimental fragments

manipulated in mesocosms under different environmental conditions.

4.02. Experimentally determine the mechanism for recruitment of patches

(clones), and maximum dispersal distances of vegetative fragments. Use

this information to determine the number of self-sustaining populations

necessary to ensure their presence throughout the range.

4.03. Experimentally manipulate in the laboratory or mesocosm, light,

temperature, salinity, and nutrients to determine their effects on flowering

and growth of vegetative fragments. 
3.2-21

4.04. Collect and transplant fruits of H. johnsonii to determine whether fruits of

H. johnsonii germinate and whether apomixis occurs.

5.01. Establish and convene an Implementation Team to develop a long-term

research plan for the species and coordinate implementation of recovery

plan actions. 

5.02. Recommend to Federal and state agencies that they adopt sampling

protocols for H. johnsonii for the permit application and monitoring

requirements of project sites (see Appendix III).

5.03. Incorporate pre- and post-construction (of in- and over-water structures) 

monitoring data of H. johnsonii distribution and abundance, from federal,

state, and local agencies, into a centralized GIS tracking system to

improve protection and management and to determine cumulative

impacts.

5.04. Provide educational opportunities and workshops for federal, state, and

local permitting agencies, including training in field identification,

sampling protocols, and the identification of designated critical habitat.

5.05 Establish federal and state interagency coordination during the permit

review process (e.g., NMFS, COE, FDEP, SJRWMD, SFWMD, FWC) for

projects that may affect H. johnsonii or its habitat so that impacts to the

species can be avoided or minimized.

5.06. Improve or maintain water quality and sediment conditions appropriate for

continuous vegetative growth and reproduction of natural populations of

H. johnsonii throughout its geographic range, addressing point and nonpoint sources and water quality-based targets (PLRGs and TMDLs). 

Coordinate these actions with existing programs, including, but not

exclusively, the Indian River Lagoon National Estuary and SWIM

programs and the Lake Worth Management Plan.

5.07. Establish PLRGs and develop TMDLs for a specific water body or

segment within a water body, describing the management actions required

to reach these guidelines (including stormwater treatment, wastewater

reuse, and best management practices for upland use).

5.08. Monitor water bodies, or the segments within, for the predicted responses

of water quality and seagrass to the implementation of water quality
3.2-22

management actions and assess the effectiveness of these specific

management actions.

5.09. Assess current federal, state, and local seagrass protection regulations and

programs (specifically those addressing human activities on submerged

lands and within the boundaries of federally-designated areas) for their

level of effectiveness in protecting H. johnsonii and its habitat. 

5.10. Assess enforcement efforts of existing submerged lands/seagrass

protection regulations to determine their effectiveness in protecting H.

johnsonii. Implement modifications to increase effectiveness of

enforcement actions, if needed. 

5.11. Preserve natural shoreline buffers on waterfront properties and encourage

shoreline restoration.

5.12. Identify and recommend the acquisition of privately-owned submerged

land vegetated with H. johnsonii and its adjacent uplands through local,

regional, state and federal programs. Public acquisition of these few tracts

will preserve the seagrass habitat associated with them and provide upland

watershed buffer protection.

5.13. Implement a multi-agency approach management program to reduce prop

scarring and trampling of shallow water seagrass beds. The management

program should use multiple methods including increased boater

education, installation of channel markers, active enforcement, and the

establishment of limited motoring zones or closure areas.

5.14. Determine whether specific protective regulations for H. johnsonii will be

developed under section 4(d) of the ESA in order to provide for the

conservation of the species.

5.15. Establish “adverse modification” and “jeopardy” guidelines for H.

johnsonii for use in section 7 consultation under the ESA.

6.01. Determine the range of genetic variability and identify genetically unique

populations within the species' geographic range.

6.02. Determine whether indices of genetic diversity are correlated with species

persistence. 
3.2-23

7.01. Conduct mesocosm and field experiments to test the feasibility of

transplanting excavated and naturally-dislodged vegetative fragments of

H. johnsonii under a broad range of environmental conditions.

7.02. Identify populations of H. johnsonii which grow and survive under

different field transplanting conditions.

7.03. Use reciprocal field and mesocosm transplants to test the effects of

different water depths, salinities, geographical ranges, and genetic stocks

in controlling the distribution and abundance of H. johnsonii. Identify key

growth and demographic characteristics that distinguish the source and the

surviving transplant populations.

7.04. Develop a reliable methodology for transplanting H. johnsonii.

7.05. Use mesocosms to maintain and experimentally test the superiority of

stock characteristics of H. johnsonii.

8.01. Develop a Web Page for H. johnsonii and post updates on its recovery

efforts.

8.02. Adapt existing education tools such as pamphlets and brochures on

Florida seagrasses to address H. johnsonii protection.

8.03. Coordinate with federal, state, and local agencies, conservation groups,

plant societies, commercial and recreational boaters and fishers, SCUBA

divers, and media to develop a positive understanding of seagrasses and

H. johnsonii.

8.04. Develop and evaluate educational materials and curricula with schools and

local environmental centers that introduce students to seagrasses, making

sure to incorporate information on H. johnsonii, its habitat, and the ESA.

8.05. Develop and present state/federal/Water Management District regulatory

workshops on survey protocol, effects of actions on H. johnsonii, and

basic biology and proper identification of the species.
4.0-1

4.0 IMPLEMENTATION SCHEDULE

Priorities in Column 1 of the Implementation Schedule are assigned as follows:

Priority 1 - An action that must be taken to prevent extinction or to prevent the

species from declining irreversibly in the foreseeable future.

Priority 2 - An action that must be taken to prevent a significant decline in species

population/habitat quality or some other significant negative impact short

of extinction.

Priority 3 - All other actions necessary to provide for full recovery of the species. 
4.0-2

Abbreviations for Implementation Schedule

BPSM FWC/Bureau of Protected Species Management

CAMA Bureau of Coastal and Aquatic and Managed Areas 

CARL Conservation and Recreation Lands

COE U.S. Army Corps of Engineers

DERM Department of Environmental Resources Management

ESA Endangered Species Act

DGPS Differential Global Positioning System

FDACS Florida Department of Agriculture and Consumer Services

FDEP Florida Department of Environmental Protection

FWC Florida Fish and Wildlife Conservation Commission

FMRI FWC/Florida Marine Research Institute

GIS Geographic Information System

HBOI Harbor Branch Oceanographic Institute

NEP National Estuary Program

NGOs Non-governmental Organizations

OCAMA FDEP/Office of Coastal and Aquatic Managed Areas 

OIS FWC/Office of Information Services 

NOAA National Oceanographic and Atmospheric Association

PLRGs Pollution Load Reduction Goals

RFP Request For Proposals

SJRWMD St. Johns River Water Management District

SFWMD South Florida Water Management District

SWIM Surface Water Improvement and Management

UNC-Wilm. University of North Carolina - Wilmington

WMDs SJRWMD and SFWMD
4.1-1

4.1 Halophila johnsonii Implementation Schedule

IMPLEMENTATION SCHEDULE

RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

2

1.01 Develop detailed baseline

distribution maps. 

2-3 yrs.,

repeat every

5 yrs.

NOAA, WMDs,

FWC/FMRI,

FDEP/CAMA,

County DERM

Offices

100 100 100 GIS and ground truthing. Build on

present database. GIS database at

NOAA or FMRI. Link with actions

2.03 and 2.04.

1.01.A Identify areas with persistent

populations.

10 yrs. NOAA,

SJRWMD,

FWC/BPSM,

County DERM

30 30 30

1.01.B Map and delineate areas with

flowering populations.

5-10 yrs. NOAA,

FWC/FMRI

10-15 10-15 10-15 Diver survey for 1 month/year, GIS. 

Develop and issue request for

proposals. 

1.01.C Identify areas of abundance or areas

that are conducive to the survival of

the species

2 yrs. NOAA,

FWC/FMRI,

WMDs

link with Actions 1.01A and 1.01B. 

1 1.02 Protect the geographic extremes of

the range and genetically unique

populations.

continuous NOAA, FDEP,

WMDs,

FWC/FMRI, 

50 50 Cost depends on level of protection.

Incorporate into regulatory process.

2 2.01 Determine whether the distribution

and size of beds are expanding or

declining and identify factors

influencing expansion or decline.

10 yrs. NOAA, WMDs, 

COE

30 30 30 Annual monitoring part of action

2.04. Develop GIS database.
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-2

2 2.02 Determine the precise northern and

southern distributional limits of H.

johnsonii and monitor the temporal

variation in these limits using DGPS

and in-situ sampling.

10 yrs.,

continuing

NOAA,

SJRWMD,

County DERM, 

5 5 5 Annual patch mapping, GIS. Link

with actions 1.01, 2.03, and 2.04.

2 2.03 Determine whether patch size,

abundance, or spacing vary from

north to south and identify if there

are presently any large distribution

gaps. 

3-5 yrs. NOAA, WMDs,

FWC/FMRI,

County DERM 

150 150 150 GIS, Link with action 1.01.

2 2.04 Monitor persistence. Establish

permanent monitoring plots at (a)

the northern and southern

distribution limits, (b) the

geographic extremes of the natural

lagoon systems within the known

geographic range, (c) sites with

existing or long-term water quality

data, and (d) sites identified to have

unique genotypes present.

10 yrs. 

continuous

NOAA, WMDs,

FDEP/OCAMA,

County DERM 

100-120 100 100 Sampled once/year. Link with action

2.02.

3 3.01 Identify sites with and without H.

johnsonii. At these, conduct a

correspondence analysis between H.

johnsonii distribution/abundance

and environmental factors (habitat

characteristics) including;

temperature, salinity, light intensity,

water motion, tidal exposure,

sediment characteristics and

stability, and eutrophication.

2 -5 yrs. NOAA, WMDS, 

County DERM, 

FWC/FMRI

100 100 50 GIS statistical analyses. Part of 

baseline. 

Link with actions 1.01, 2.02, 3.02,

and 7.01-7.03.
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-3

3 3.02 Locate ephemeral populations of H.

johnsonii and identify the

characteristics (as determined by

3.01) of these sites.

>5 yrs.

NOAA, WMDS, 

FWC/FMRI

30 30 Combine with actions 1.01, 1.02,

3.01, and 3.03. 

3 3.03 Identify the habitat characteristics

which favor populations with female

flowers (assuming male flowers

should co-occur with females) and

experimentally manipulate these

conditions in the laboratory or

mesocosm to attempt to induce

flowering.

2 yrs. NOAA,

FWC/FMRI

15 10 10 Combine with action 3.04, and 101.A.

First need to determine if female

flowers contribute to recruitment. 

3 3.04 Conduct experiments to determine

the effect of other seagrass species

on the distribution and abundance

ofH. johnsonii and assess the

similarity of habitat requirements

between H. johnsonii and other

species.

2-5 yrs. NOAA, COE, 

FWC/FMRI

50 50 50 Combine with action 3.02. In-situ and

mesocosm experiments. Develop and

issue request for proposal: grant,

contract. 

3 3.05 Determine if water quality and water

management programs are

appropriate for determining changes

in conditions which would affect the

continuous vegetative growth and

reproduction of H. johnsonii.

1-2 yrs. NOAA, FDEP,

WMDs 

20-30 20-30
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-4

3 3.06 Select areas throughout the

geographic range of the species

which have suitable environmental

conditions for perennial and

flowering populations for use in the

development and management of

special protection areas for H.

johnsonii.

1-2 yrs. NOAA, FDEP,

FWC, COE

15 10 Establish preserve in critical areas. 

Possibly National Estuarine Research

Reserve. Link with Action 5.13.

2 4.01 Estimate rates of new shoot (the

vertical shoot formed by the

branching of the horizontal

rhizome/apical meristem) formation

and death rates in natural

populations and in experimental

fragments manipulated in

mesocosms under different

environmental conditions.

2-3 yrs.

NOAA

50 30 30 Action 4.01 to be combined with

action 4.02 in same study.

Develop and issue request for

proposal: grant, contract. 

1 4.02 Experimentally determine the

mechanism for recruitment of

patches (clones) and maximum

dispersal distances of vegetative

fragments. Use this information to

determine the number of selfsustaining populations necessary to

ensure their presence throughout the

range.

3-5 yrs. NOAA,

FWC/FMRI 

30 30 To be combined with action 4.01 in

same study. 

2 4.03 Experimentally manipulate in the

laboratory or mesocosm, light,

temperature, salinity and nutrients to

determine their effects on flowering

and growth of vegetative fragments.

2-3 yrs. NOAA,

FWC/FMRI

40 20 20 Mesocosm experiments. Develop and

issue request for proposal: grant,

contract. 
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-5

2 4.04 Collect and transplant mature fruits

of H. johnsonii to determine

whether fruits of H. johnsonii

germinate and whether apomixis

occurs. 

1-3 yrs. NOAA

25

Link with action 7.02. 

Also individual monitoring of plants.

Develop and issue request for

proposal: grant, contract. 

2 5.01 Establish and convene an

Implementation Team to develop a

long-term research plan for the

species and coordinate

implementation of recovery plan

actions.

semiannuallyNOAA, WMDs,

FWC/FMRI,

FDEP, COE

25 25 25 To begin immediately.

2 5.02 Recommend to Federal and state

agencies that they adopt sampling

protocols for H. johnsonii for the

permit application and monitoring

requirements of project sites

(Appendix III).

1-2 yrs. FDEP, WMDs,

COE, 

FWC/BPSM

1 1 1 Costs are for agency/public

workshops. 

2 5.03 Incorporate pre- and postconstruction monitoring data of H.

johnsonii distribution and

abundance, from federal, state, and

local agencies, into a centralized

GIS tracking system to improve

protection and management and to

determine cumulative impacts.

1-2 yrs, 

ongoing

NOAA (and

contractor), COE, 

FDEP, WMDs

25 25 Put into permit requirement. Should

be done in conjunction with actions

2.04 and 8.04.

 Requires setting up GIS database.

3 5.04 Provide educational opportunities

and workshops for federal, state, and

local permitting agencies, including

training in field identification,

sampling protocols, and critical

habitat. 

Periodic

intervals

annually

NOAA, COE,

FDEP, WMDs,

FWC/BPSM

25 25 Cross-reference with actions 8.01-

8.05. Link with action 5.02.

(10K-meeting; 20K - Employee)

Costs to hold workshop in year 1 and

print brochure in year 2. 
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-6

1 5.05 Establish federal and state

interagency coordination during the

permit review process (e.g., NOAA,

COE, FDEP, SJRWMD, SFWMD,

FWC) for projects that may affect H.

johnsonii or its habitat so that

impacts to the species can be

avoided or minimized.

6-9 months, 

within 1 

year

NOAA, COE,

FDEP, WMDs,

FWC/BPSM

10 Travel costs for meeting to establish

the process, likely out of agencies’

existing funds. 

1 5.06 Improve or maintain water quality

and sediment conditions appropriate

for continuous vegetative growth

and reproduction of natural

populations of H. johnsonii

throughout its geographic range,

addressing point and non-point

sources and water quality-based

targets (PLRGs and TMDLs). 

Coordinate these actions with

already existing programs,

including, but not exclusively, the

Indian River Lagoon National

Estuary and SWIM programs, and

the Lake Worth Management Plan.

Initially 1-2 

yrs.,

continuous

FDEP, WMDs,

NEP

Incorporate, where feasible, into

currently existing regulations.Link

with action 5.07.

2 5.07 Establish Pollutant Load Reduction

Goals (PLRGs) and determine Total

Maximum Daily Loads (TMDLs)

for specific water body or segment

within a water body, describing the

management actions required to

reach these guidelines (including

stormwater treatment, wastewater

reuse, and best management

practices for upland use). 

5 yrs. FDEP, WMDs 20 Link with actions 3.03, 3.05, and

4.03.Being done in Indian River

Lagoon for seagrass in general.
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-7

3 5.08 Monitor water bodies, or the

segments within, for the predicted

responses of water quality and

seagrass to the implementation of

management actions. 

continuous FDEP, WMDs,

DERM

Link with actions 3.05 and 4.03. Link

with monitoring designs and costs of

action 2.04.

1 5.09 Assess current federal, state, and

local seagrass protection regulations

(specifically those that addressing

human activities on state-owned

submerged lands and within the

boundaries of federally-designated

areas) for their level of effectiveness

in protecting H. johnsonii and its

habitat.

ongoing NOAA, FDEP,

FWC

Partially addressed in Recovery Plan,

Chapter 1. Link with action 3.05.

2 5.10 Assess enforcement efforts of

existing submerged land/seagrass

protection regulations. Implement

modifications to increase

effectiveness of enforcement

actions, as needed.

6 mos.-1 yr. NOAA, FDEP,

FWC

5-10 Link with actions 3.05, 5.05 and 5.06.

3 5.11 Preserve natural shoreline buffers on

waterfront properties and encourage

shoreline restoration.

continuous FDEP, DERM ,

COE, NEP, 

WMDs, FWC

Link with action 8.01. Should be part

of FDEP, county existing programs.

3 5.12 Identify and recommend the

acquisition of privately-owned

submerged lands vegetated with H.

johnsonii and its adjacent uplands

through local, regional, state and

federal programs.

continuous WMDs, FDEP

DERM, NOAA,

NGOs

Florida Forever project. Cost depends

on acquisition costs. Use 2000

SWIM programs. Enter into baseline

GIS as acquired: action 1.01. 
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-8

3 5.13 Implement a multiple agency

management program to reduce prop

scarring and trampling of shallow 

water seagrass beds.

2-5 yrs. NOAA, NEP,

FDEP, FWC 

50 Link with ongoing FDEP efforts. 

Link with action 8.01. 

3 5.14 Determine whether specific

protection regulations for H.

johnsonii will be developed under

section 4(d) of the ESA in order to

provide for the conservation of the

species.

1-2 yrs. NOAA, FDEP,

COE, 

FWC/FMRI

Link with actions 5.05 and 5.06. 

Will assist in permitting process.

2 5.15 Establish "adverse modification"

and “jeopardy” guidelines for H.

johnsonii for use in Section 7

consultation under the ESA.

1 yr. NOAA

2 6.01 Determine the range of genetic

variability and identify genetically

unique populations within the

species' geographic range. 

1-2 yrs. NOAA 40 30 Link with actions 1.02, 2.03, 3.01,

4.02. Develop and issue request for

proposal: grant, contract. 

2 6.02 Determine whether indices of

genetic diversity are correlated with

species persistence.

up to 5 yrs. NOAA 150 100 40 Link with actions 4.01, 4.02, and 7.02

in single study.

2 7.01 Conduct mesocosm and field

experiments to test the feasibility of

transplanting excavated and

naturally-dislodged vegetative

fragments of H. johnsonii under a

broad range of environmental

conditions. 

2-3 yrs. NOAA,

contractors

40 40 20 Link with actions 4.01, 4.02, and 7.01

in single study. Develop and issue

request for proposal: grant, contract.
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-9

3 7.02 Identify populations of H. johnsonii

which grow and survive under

different field transplanting

conditions.

2-3 yrs. NOAA,

FWC/FMRI 

30 30 30 Actions 7.03, 7.04, 7.05, and 7.06 to

be combined in one request for

proposal. Link with actions 2.04,

4.02, and 4.03.

3 7.03 Use reciprocal field and mesocosm

transplants to test the effects of

different water depths, salinities,

geographical ranges, and genetic

stocks on controlling the distribution

and abundance of H. johnsonii.

Identify key growth and

demographic characteristics that

distinguish the source and the

surviving transplant populations. 

2-3 yrs. NOAA,

FWC/FMRI

75 75 75 Link with actions 2.04, 4.01, 4.02,

7.03, 7.04 and 7.06.

Develop and issue request for

proposal: grant, contract. 

3 7.04 Develop a reliable methodology for

transplanting H. johnsonii.

2-3 yrs. NOAA,

FWC/FMRI

20 20 20 In conjunction with 7.03.

3 7.05 Use mesocosms to maintain and

experimentally test the superiority of 

stock characteristics of H. johnsonii.

ongoing, 

2 -5 yrs.;

maintain 

continuously

NOAA,

FWC/FMRI

50 50 5 Link with actions 4.02, 4.03, 7.03,

7.04, and 7.05. Cost depends on

personnel. State facility maintains

stocks from 

7.03 and 7.04. Develop and issue 

request for proposal: grant, contract. 

3 8.01 Develop a Web Page for H.

johnsonii and post updates on its

recovery efforts.

4 months-1

 yr., then 

continuous

NOAA, FDEP 10 10 10 An action for an existing webmaster.
RESPONSIBLE 

PARTY

COST ESTIMATES

($K)

PRIORITY

#

ACTION

#

ACTION

DESCRIPTION

ACTION

DURATION

FY 1 FY 2 FY 3 COMMENTS/NOTES

4.1-10

3 8.02 Adapt existing education tools such

as pamphlets and brochures on

Florida seagrasses to address H. 

johnsonii.

1-2 yrs,

continuous 

supply

NOAA, FDEP,

FWC

20 20 In existing Environmental

Information (E&I)/Outreach and

Education departments. Contribute to

printing costs. Link actions 8.02,

8.03, and 8.04. 

3 8.03 Coordinate with federal, state, and

local agencies, conservation groups,

plant societies, commercial and

recreational boaters and fishers,

SCUBA divers, and media to

develop a positive understanding of

seagrass and H. johnsonii.

ongoing NOAA, FDEP,

FWC/OIS,

FDACS, NEP

minimal

but may

require

workshop

s

Use Public Relations personnel.Cost

of brochures and teaching aids. Use

existing programs.

3 8.04 Develop and evaluate educational

materials and curricula with schools

and local environmental centers that

introduce students to seagrasses,

making sure to incorporate

information on H. johnsonii, its

habitat, and the ESA.

1 yr., 

continuous

NOAA, FDEP,

FWC/OIS,

FDACS

15 Use input from actions 1.01, 2.04,

3.04, 4.03, 5.04, 5.15, 7.01, and 8.02. 

Link with essential fish habitat and

faunal survey. 

Input of Dept. of Education and local

districts 

3 8.05 Develop and present

state/federal/Water Management

District regulatory workshops on

survey protocol, effects of actions

on H. johnsonii, and basic biology

and proper identification of the

species. 

Several

times during

first year.

One every 

2-3 years.

NOAA, FDEP,

WMDs,

FWC/OIS,

FDACS

25 0 25 Link with actions 5.03, 5.04. Use

actions 1.01, 2.04, and 4.03. Needed

workshops, use existing programs. 
4.2-1

4.2 Implementation Schedule Summary

The following is a summary list of Johnson’s seagrass recovery actions in order of

priority.

Priority #

1 1.02. Protect the geographic extremes of the range and genetically

unique populations (In coordination with Section 5, Management;

and Section 6, Genetics).

1 4.02. Experimentally determine the mechanism for recruitment of

patches (clones), and maximum dispersal distances of vegetative

fragments. Use this information to determine the number of selfsustaining populations necessary to ensure their presence

throughout the range.

1 5.05. Establish federal and state interagency coordination during the

permit review process (e.g., NMFS, COE, FDEP, SJRWMD,

SFWMD, FWC) for projects that may affect H. johnsonii or its

habitat so that impacts to the species can be avoided or minimized.

1 5.06. Improve or maintain water quality and sediment conditions

appropriate for continuous vegetative growth and reproduction of

natural populations of H. johnsonii throughout its geographic

range, addressing point and non-point sources and water qualitybased targets (PLRGs and TMDLs). Coordinate these actions with

existing programs, including, but not exclusively, the Indian River

Lagoon National Estuary and SWIM programs and the Lake Worth

Management Plan.

1 5.09. Assess current federal, state, and local seagrass protection

regulations and programs (specifically those addressing human

activities on submerged lands and within the boundaries of

federally-designated areas) for their level of effectiveness in

protecting H. johnsonii and its habitat.

2 1.01. Develop detailed baseline distribution maps (In coordination with

Section 2, Monitoring).
4.2-2

1.01.A. Identify areas with persistent populations.

1.01.B. Map and delineate areas with flowering populations.

1.01.C. Identify areas of high abundance or areas that are conducive to 

 the survival of the species. 

2 2.01. Determine whether the distribution and size of beds are expanding

or declining and identify factors influencing expansion or decline. 

2 2.02. Determine the precise northern and southern distributional limits

of H. johnsonii and monitor the temporal variation in these limits

using DGPS and in-situ sampling. 

2 2.03. Determine whether patch size, abundance, or spacing vary from

north to south, and identify if there are presently any large

distribution gaps (see Protect Populations and Habitat section).

2 2.04. Monitor persistence. Establish permanent monitoring plots at (a)

the northern and southern distribution limits, (b) the geographic

extremes of the natural lagoon systems within the known

geographic range (i.e., the southern end of the IRL and the

northern end of Lake Worth), (c) sites with existing or long-term

water quality data, and (d) sites identified to have unique or

diverse genotypes present (e.g., Boynton Beach, Boca Raton, etc.).

Annual monitoring should be conducted for 10 years to determine

whether criteria for de-listing have been met. 

2 4.01. Estimate rates of new short shoot (the vertical shoot formed by the

branching of the horizontal rhizome/apical meritstem) formation

and death rates in natural populations and in experimental

fragments manipulated in mesocosms under different

environmental conditions.

2 4.03. Experimentally manipulate in the laboratory or mesocosm, light,

temperature, salinity, and nutrients to determine their effects on

flowering and growth of vegetative fragments. 

2 4.04. Collect and transplant fruits of H. johnsonii to determine whether

fruits of H. johnsonii germinate and whether apomixis occurs.
4.2-3

2 5.01. Establish and convene an Implementation Team to develop a longterm research plan for the species and coordinate implementation

of recovery plan actions. 

2 5.02. Recommend to Federal and state agencies that they adopt sampling

protocols for H. johnsonii for the permit application and

monitoring requirements of project sites (see Appendix III).

2 5.03. Incorporate pre- and post-construction (of in- and over-water

structures) monitoring data of H. johnsonii distribution and

abundance, from federal, state, and local agencies, into a

centralized GIS tracking system to improve protection and

management and to determine cumulative impacts.

2 5.07. Establish PLRGs and develop TMDLs for a specific water body or

segment within a water body, describing the management actions

required to reach these guidelines (including stormwater treatment,

wastewater reuse, and best management practices for upland use).

2 5.10. Assess enforcement efforts of existing submerged lands/seagrass

protection regulations to determine their effectiveness in protecting

H. johnsonii. Implement modifications to increase effectiveness of

enforcement actions, if needed. 

2 5.15. Establish “adverse modification” and “jeopardy” guidelines for H.

johnsonii for use in section 7 consultation under the ESA.

2 6.01. Determine the range of genetic variability and identify genetically

unique populations within the species' geographic range.

2 6.02. Determine whether indices of genetic diversity are correlated with

species persistence. 

2 7.01. Conduct mesocosm and field experiments to test the feasibility of

transplanting excavated and naturally-dislodged vegetative

fragments of H. johnsonii under a broad range of environmental

conditions.

3 3.01. Identify sites with and without H. johnsonii. At these sites,

conduct a correspondence analysis between H. johnsonii

distribution/abundance and environmental factors (habitat
4.2-4

characteristics) including: temperature, salinity, light intensity,

water motion, tidal exposure, sediment characteristics and

stability, and eutrophication (Also see Actions 7.01, 7.02 and

7.03).

3 3.02. Locate ephemeral populations of H. johnsonii and identify the

characteristics (listed in Action 3.01) of these sites.

3 3.03. Identify the habitat characteristics which favor populations with

female flowers (assuming male flowers should co-occur with

females) and experimentally manipulate these conditions in either

the laboratory or mesocosm to attempt to induce flowering.

3 3.04. Conduct experiments to determine the effect of other seagrass

species on the distribution and abundance of H. johnsonii and

assess the similarity of habitat requirements between H. johnsonii

and other species.

3 3.05. Determine if water quality and water management programs are

appropriate for determining changes in conditions which would

affect the continuous vegetative growth and reproduction of H.

johnsonii.

3 3.06. Select areas throughout the geographic range of the species which

have suitable environmental conditions for perennial and flowering

populations for use in the development and management of special

protection areas for H. johnsonii (In coordination with Action

5.13).

3 5.04. Provide educational opportunities and workshops for federal, state,

and local permitting agencies, including training in field

identification, sampling protocols, and the identification of

designated critical habitat. 

3 5.08. Monitor water bodies, or the segments within, for the predicted

responses of water quality and seagrass to the implementation of

water quality management actions and assess the effectiveness of

these specific management actions.

3 5.11. Preserve natural shoreline buffers on waterfront properties and

encourage shoreline restoration.
4.2-5

3 5.12. Identify and recommend the acquisition of privately-owned

submerged land vegetated with H. johnsonii and its adjacent

uplands through local, regional, state and federal programs. Public

acquisition of these few tracts will preserve the seagrass habitat

associated with them and provide upland watershed buffer

protection.

3 5.13. Implement a multi-agency approach management program to

reduce prop scarring and trampling of shallow water seagrass beds. 

The management program should use multiple methods including

increased boater education, installation of channel markers, active

enforcement, and the establishment of limited motoring zones or

closure areas.

3 5.14. Determine whether specific protective regulations for H. johnsonii

will be developed under section 4(d) of the ESA in order to

provide for the conservation of the species.

3 7.02. Identify populations of H. johnsonii which grow and survive under

different field transplanting conditions.

3 7.03. Use reciprocal field and mesocosm transplants to test the effects of

different water depths, salinities, geographical ranges, and genetic

stocks in controlling the distribution and abundance of H.

johnsonii. Identify key growth and demographic characteristics

that distinguish the source and the surviving transplant

populations.

3 7.04. Develop a reliable methodology for transplanting H. johnsonii.

3 7.05. Use mesocosms to maintain and experimentally test the superiority

of stock characteristics of H. johnsonii.

3 8.01. Develop a Web Page for H. johnsonii and post updates on its

recovery efforts.

3 8.02. Adapt existing education tools such as pamphlets and brochures on

Florida seagrasses to address H. johnsonii protection. 

3 8.03. Coordinate with federal, state, and local agencies, conservation

groups, plant societies, commercial and recreational boaters and
4.2-6

fishers, SCUBA divers, and media to develop a positive

understanding of seagrasses and H. johnsonii.

3 8.04. Develop and evaluate educational materials and curricula with

schools and local environmental centers that introduce students to

seagrasses, making sure to incorporate information on H.

johnsonii, its habitat, and the ESA.

3 8.05. Develop and present state/federal/Water Management District

regulatory workshops on survey protocol, effects of actions on H.

johnsonii, and basic biology and proper identification of the

species.
5.0-1

5.0 REFERENCES

Atlantic States Marine Fisheries Commission. 1997. ASMFC Habitat Statement and

SAV Policy Statement and Implementation Plan. Washington, D.C.

Bjorndal, K. 1981. Biology and Conservation of Sea Turtles. Smithsonian Institute

Press, Washington.

Bolen, L.E. 1997. Growth dynamics of the seagrass Halophila johnsonii from a

Subtropical estuarine lagoon in southeastern Florida, USA. M.S. Thesis. Florida 

Atlantic University, Boca Raton, Florida. 

Bureau of Protected Species Management, FWC. February 2000. Palm Beach County

Seagrass Survey, version 1.0. CD-Rom.

Dawes, C.J., C.S. Lobban, and D.A. Tomasko. 1989. A comparison of the physiological

ecology of the seagrasses Halophila decipiens Ostenfeld and H. johnsonii

Eiseman from Florida. Aquat. Bot. 33:149-154.

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A.I.-1

APPENDIX I

Listing Notice for Halophila johnsonii

Federal Register 63(177): 49035
A.I.-2

— Insert FR notice here
A.II.-1

APPENDIX II

Notice for Critical Habitat for Halophila johnsonii

Federal Register 65(66): 17786
A.II.-2

–Insert FR notice here
A.III.-1

APPENDIX III

Recommendations for sampling Halophila johnsonii

at a project site
A.III.-2

Recommendations for sampling Halophila johnsonii at a project site

The following suggested approaches for sampling H. johnsonii are recommendations of

the H. johnsonii Recovery Team.

OBJECTIVE:

To outline recommended survey methods for determining the distribution and abundance

of H. johnsonii at sites under permit review. The methods should be applicable to a

broad range of project scales, from a 20-m long dock, to marinas, bridges, and channels

several kilometers long.

PROBLEM:

Three aspects make quantitative sampling for H. johnsonii difficult: (1) Poor visibility; it

is sometimes difficult to see more than 0.1 or even 0.01 m2 at a time. (2) Patchy and

clumped distribution, with patches as small as 0.01 m2, which may be clumped together

within a sub-area of the project area. (3) Stratified distribution, with occurrence perhaps

limited to a particular depth gradient within a project area.

RECOMMENDED METHODS: The most appropriate approach depends on scale, and

the amount of expected error depends on the approach. Unless a complete survey of the

entire area is done, the estimated distribution and abundance of this species may be

significantly in error. With the exception of very small project areas, efficient field
A.III.-3

sampling may require sampling in two stages. A preliminary visual reconnaissance of

the site should be conducted to locate any occurrences of H. johnsonii. “The importance

of preliminary sampling is probably the most under emphasized principal related to field

studies. There is no substitute for it.” (Green 1979). Following the preliminary

reconnaissance, a more comprehensive sampling, using one of the techniques outlined

below, should be initiated. In situ monitoring for H. johnsonii is absolutely necessary. 

Aerial photography may be used to map distributions of larger canopy-forming species;

however, mapping of H. johnsonii cannot be done reliably from aerial photos. Because

of significant seasonal and annual variation in distribution and abundance of H.

johnsonii, surveys must be conducted during spring/summer (April 1 to August 31)

period of maximum abundance, and sampling in more than one summer is recommended. 

Length of time between survey date and actual start of project should consider the

potentially rapid turnover and migration of H. johnsonii. Personnel conducting the

survey should clearly demonstrate that they can distinguish between H. johnsonii and H.

decipiens. Surveys labeled simply as “Halophila” are not sufficient.

Deliverables: 1) amount (acres or square meters) impacted, 2) estimate of percent

coverage and the species present/absent, 3) site map with seagrass patch or bed locations,

4) size of the patches, and, as feasible, 5) shoot density estimate.

SMALL PROJECT SITES (<0.1 ha, e.g. 10 m by 100 m, such as single-family docks). 

Two methods.
A.III.-4

1. Provide a site map of submerged lands adjacent to the action area. The site map

should include transects approximately every 7.5 m apart, perpendicular to the shore, and

for a length 6 m longer than the proposed activity. A preliminary visual reconnaissance

is necessary to fill in the information between the transects. Seagrass patches should be

identified by species composition and drawn on the site map. Density can be

accomplished with random sub-sampling for density within the identified patches. (An

overall site map is important since it identifies seagrass habitat, not just existing seagrass

patches. (Mezich pers. comm. 2000)).

2. The site is sub-divided into m2 grids. A complete and intensive mapping of the entire

area of concern can be developed by using DGPS, with coordinates provided every m2, or

every patch >0.01-0.1 m2, with a tested map accuracy of >50-95%. If percent cover is

not used, an illustrated, standardized scale of density should be used. Presence-absence

should be determined for every m2 grid cell.

INTERMEDIATE-AREA PROJECT SITES (0.1 to 1 ha, e.g., a 100-mby 100-m

marina). A two-step process is required.

a. Preliminary visual reconnaissance to locate general H. johnsonii areas and

distribution.

b. The site should then be surveyed using transects across the dominant spatial gradients 

(e.g., depth, inshore-offshore, channel-shoal, etc.) of the site. The number of transects

and sample intervals should adequately describe distribution and abundance of H.
A.III.-5

johnsonii patches. Besides noting presence-absence, x-y diameters, e.g., north-south or

parallel-perpendicular to shore, of encountered patches should be noted. As possible,

sub-samples of shoot density, blade length, and presence of flowering could also be

recorded.

LARGE-AREA PROJECT SITES (>1 ha). Three choices are possible after preliminary

visualreconnaissance.

1. Random sampling of points or quadrats within the area.

Sampling at least 10-30% of the total area.

• 2 stages: (1) visual reconnaissance, then stratify, (2) second intensive sampling,

with intensity relative to abundance of H. johnsonii within the strata.

• singe step of 100 -1,000 points/quadrats (minimum [min.] # = ?). 

2. Intensive survey of transects.

Transects across the entire area, sampling at least 10-30% of the total area.

• point-intersect sampling along transects (with the size of a “point” defined, e.g., 5

x 5 or 10 x10 cm). 

• belt transect, of 0.1-2 m width.

• transects randomly located (min. # transects = 10-50 or min. spacing = 50 m).

• regularly-spaced transects (min. # transects = 10-50 or min. spacing = 50 m).

• quadrats at regular intervals along line (min. # = 10-50 or min. spacing = 50 m).
A.III.-6

For any of these transect methods, x-y diameters of any patches encountered should be

measured. At a minimum, presence-absence should be recorded at each point or each

quadrat.

3. Combinations of above methods, e.g.,

(a) Intensive mapping in area of primary impact (e.g., within footprint of proposed

dock), plus random points in surrounding, potentially affected area.

(b) Stratify from random point sampling, then map intensively in areas of greatest

abundance.

It is the position of the Recovery Team, however, that the adoption of a valid survey

protocol for identifying Johnson's seagrass be required by permitting agencies in the

range of the species. In all seagrass surveys, emphasis should be placed on the

identification of seagrass habitat as well as the distribution of currently existing patches. 

References

Green, R.H. 1979. Statistical design and statistical methods for environmental

biologists. John W. Wiley and Sons, Inc., New York. 

Mezich, Ron 2000. Personal Communication. Florida Freshwater and Wildlife

Conservation Commission, Marine Resources, Tallahassee, Florida.