GEOLOGICAL SURVEY CIRCULAR 677 

A Review of Benthic Faunal Surveys 

in San Francisco Bay 

A Review of Benthic Faunal Surveys 

in San Francisco Bay 

By Frederick H. Nichols 

G E 0 l 0 G I C A l S U R V E Y C I R C U l A R 677 

Washington 1973 
United States Department of the Interior 

ROGERS C. B. MORTON, Secretary 

Geological Survey 

V. E. McKelvey, Director 

Free on application to the U.S. Geological Survey, Washington, D.C. 20244 
CONTENTS 

Abstract 

Introduction ----------------------------------------------------------------------------------------------------------------------------------

Surveys of benthic organisms in San Francisco Bay ------------------------------------------------------------

Historical review --------------------·············----------------····-·····-·-------------···--·----··-·------------------------

Summary ·-----------·---------·----·-----------------·-------········-------------------·------------------------------·'·-------------

Inadequacies of existing data-·--····-·····-··---··-------·------------·-------------------------------------------,·-------------

Sampling methodology·····--·····--------··--·-------------------·----------------------------·-··-----------··-------------

Species identifications and Jife history studies ----·-------------------------·-··················-------------

Effect of pollutants on benthic animals-the diversity index ---·------------------··-------------

Proposed directions of future research --·------·------------------------·--------------------·--------------··-------------

References -----------------------------------·---------------------------··---·--------------------------------·--·-------------·-------------

ILLUSTRATION 

Page 

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9 

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FIGURE L Sketch map of San Francisco Bay estuary-------·········---------------------------·-··-··---···· 3 

TABLE 

Page 

TABLE 1. Summary of methods used in surveys of the benthic organisms of San 

Francisco Bay, arranged alphabetically by author -----·-·--····-----·····-·······--·---· 11 

III 

A Review of Benthic Faunal Surveys 

in San Francisco Bay 

By Frederic H. Nichols 

ABSTRACT 

During the past 60 years, considerable effort has been 

expended in studies of the relations of the biotic community and physicochemical characteristics of San Francisco 

Bay water. In very recent years these studies have 

emphasized the relations between the "state of health" of 

bottom-living invertebrates (the benthos) and the levels 

of pollutants in the bay. Benthic organisms, generally 

sessile, are unable to escape deleterious environmental 

changes, and they reflect these changes in alterations of 

normal species composition of assemblages and species 

abundance. Data that expands understanding of these 

relations in urbanized areas such as San Francisco Bay 

are critical. Because of the implications of such data in 

control of water quality, the U.S. Geological Survey 

undertook a review of the results and major conclusions 

of San Francisco Bay benthic surveys. 

The size and species composition of faunal assemblages 

are largely controlled by the salinity of the water, the 

texture of the bottom sediments, and locally by wastes 

discharged into the bay. Efforts to describe the structure 

and function of benthic communities of the bay and to 

quantify the effects of waste discharge on them have been 

hampered by inconsistent and often faulty sampling 

methodology and species identification. Studies made 

show a lack of information on the normal life processes 

of the organisms concerned. The diversity index (a 

mathematical expression of the number of kinds of organisms present at a location), commonly used to describe 

the "health" of the benthic community, has been 

employed without regard for the need for standardizing 

methodology and species identifications or for understanding natural biological processes that affect such 

mathematical indices. There are few reliable quantitative 

data on the distribution of benthic organisms in San 

Francisco Bay with which future assessments of the 

"health" of the benthic community might be compared. 

Methods for study of the benthos must be standardized, 

identifications of species verified by trained taxonomists, 

and new field and laboratory studies undertaken before 

we can expect to obtain an accurate description of the 

benthic fauna and its relations with the environment. 

1 

INTRODUCTION 

Prior to the mid-19th century, the f'lln Francisco Bay area was rich in fish and sheJlfish, providing iood and livelihood for inhabitants of the 

region. The late 1800's brought about intensive 

commercial exploitation of these fisheries; for 

example, in 1880, 21 salmon canneries processed 

10 million pounds of salmon, and in 1892 nearly 3 

million pounds of crab and more than 5 million 

pounds of shrimp were caught (Skinn~r, 1962). 

Seafood harvested in 1899 included 1 million 

pounds of striped bass and nearly 3 milli'ln pounds 

of oysters, many species of which were introduced 

by man in the latter half of the 19t-, century 

(Skinner, 1962). These bountiful harvests began 

to decline before the beginning of this century 

owing to overfishing, pollution, and siltation, in 

part from hydraulic gold mining in the drainage 

area above the bay (Skinner, 1962). Tr~ bay was 

not only a primary source for man's foul but was 

becoming his waste receptacle as well. The 

decrease in productivity of the fisherieF resources 

of the bay was so rapid that in 1912 a m!ljor scientific investigation, the Albatross Expecition, was 

launched to study the causes. The inhabitants of 

the bay area clearly understood that man was 

having a deleterious effect on the biota of the bay 

and that the bay was in a state of declining 

"health." 

Since the time of the Albatross Expedition of 

1912-13, the concern of scientists and laymen has 

led to numerous investigations of the biota of the 

bay and the relations between the characteristics 

of the aquatic environment (natural and manmade) and the biota. Recently, large-scale surveys 
have been conducted at considerable public expense to determine how waste discharges affect 

the biota, to establish the means by which the 

obvious decline of the fishery resources might be 

reversed, and to suggest ways to improve water 

quality in the bay. 

Many legislative decisions affecting the control 

of San Francisco Bay water quality are now being 

made or soon will be. It is critical to examine what 

is understood about the biological processes of the 

bay and to carefully decide what ought to be 

known before establishing realistic long-range 

goals. That fishery resources have been drastically 

reduced by man's use and misuse of the bay is 

clear; the precise cause and nature of this reduction is not clear. Even less clear is the specific 

nature of the means necessary to reverse the trend. 

In this report an attempt is made to point out 

wherein past efforts to answer these questions 

have been unsatisfactory and to emphasize the 

need for more appropriate investigations into the 

causal relations between the "health" of the biota 

and the environment in which it must exist. 

This report is restricted in scope to a critical 

summary of the methods, results, and general conclusions of those biological surveys conducted in 

the bay concerned with the macroinvertebrate 

organisms (organisms larger than some finite size, 

for example, 0.5 mm) living at the bottom of the 

bay (the benthos). Macro benthic organisms are 

generally sessile (live most of their lives in the 

same location) and longlived (several months to 

several years) and as such are unable to escape 

deleterious environmental changes. They are 

therefore indicators of the "health" of the bay; 

that is, any group or assemblage of species reflects 

the cumulative effect of exposure to the environment, recording by changes in species composition or abundance the effects of both short- and 

long-term changes in the environment. 

This review does not include a summary of 

those studies concerned with marine boring and 

fouling organisms (animals that bore into or 

encrust pilings, wharfs, ship bottoms; see for 

example, Hill and Kofoid, 1927, and the studies 

cited therein; Graham and Gay, 1945; Filice, 

1954a) or those concerned with salt-pond organisms (Carpelan, 1957). Nor does it review very 

recent studies that evaluate local effects of individual waste discharges on the nearby biota, for 

the results of these studies, required by California 

State law (see California Water Resources Con2 

trol Board, 1972b) and conducted by private 

firms, are not yet readily available t1 the general 

public. 

I greatly appreciate the helpful crJ~ticism of Dr. 

Karl Banse, Department of Oceano~raphy, University of Washington; Dr. Joel '\Y. Hedgpeth, 

Department of Oceanography, Oregc'l State University; James T. Carlton, Department of Invertebrate Zoology, California Academy of Sciences; 

and my colleagues of the U.S. Geoloncal Survey. 

J. T. Carlton has been especially hel:>ful in locating some of the material discussed h~rein. 

SURVEYS OF BENTHIC ORGANISMS IN 

SAN FRANCISCO BAY 

HISTORICAL REVIEW 

The first major investigation of tl·~ biology of 

the bay began in 1912 under the au~Dices of the 

Federal Bureau of Fisheries. Scientists participating this investigation aboard the research vessel 

Albatross collected samples of the bottom fauna, 

water, and sediments at stations throughout the 

bay during 1912 and 1913 to estimate the existing 

and potential market value of the commercial fisheries and to obtain knowledge concerning the 

biological and physical conditions up'ln which the 

fisheries depend. These scientists were especially 

interested in explaining the decline of the oyster 

industry during the decade prior to this survey. 

Benthic animals were collected in many "qualitative" dredge samples taken during the 14-month 

study and in a few ( 43) "quantitative" orangepeel grab samples (Sumner and others, 1914) 

taken between December 1912 and February 1913. 

(In this report grab is used as in Thc.rson (1957) 

to denote those samplers that take a r0int sample, 

as distinguished from a dredge, which is dragged 

on the bottom for some distance, tal-ing an integrated sample.) Some of the bay mor·1sks (clams 

and oysters), at least partly because of their commercial value, received the most thorc•Ighly quantitative study (Packard, 1918a and b). Packard 

noted that the distribution of mollu~~an species 

was in part regulated by salinity, for most marine 

species were found only below Carquinez Strait 

(fig. 1). Because salinity was low above the strait, 

only a meager fauna existed in the brackish water. 

But the most significant environmental influence 

on molluscan distribution appeared to be the texture of bottom sediments (particle size, shape, 

and arrangement). Sediment com pored of mixed 

mud, sand, and (or) gravel (central bay) sup-
FIGURE 1.-San Francisco Bay estuary. 

ported the greatest number of species, mud (San 

Pablo and south bays) fewer species but a greater 

number of individuals. 

Packard's study of the molluscan fauna ( 1918a, 

b) provided the baseline for most benthic investigations that followed. His species lists and relative abundances of specimens for those species 

have formed the basis for qualitative judgements 

on long-term changes of the fauna of the bay, 

despite the fact that his samples were nonquantitative, as discussed in the section "Inadequacies 

of Existing Data." 

Of the remaining benthic fauna collected during 

the Albatross Expedition, only the decapod crustaceans (shrimps, crabs) received comprehensive 

attention. Within a larger study of the decapod 

crustacea of California, Schmitt ( 1921) described 

the occurrence and geographic distribution of 4 7 

3 

species of decapods collected in the Albatross 

dredge and grab samples. He confirmed Packard's 

(1918b) findings that organisms were distributed 

according to salinity and sediment characteristics, 

not depth or water temperature. Although the 

samples from which the species of crustaceans 

were identified were generally nonquantitative 

(abundances not calculated on an areal basis), 

Schmitt's study, together with Packard's, provides the first thorough description of a portion of 

the benthic fauna of San Francisco Bay. The other 

benthic specimens from the Albatross Expedition 

have apparently been scattered among many museum or private collections, resulting in the publication of numerous short reports concerning the 

taxonomy of individual species or groups of species 

(for example, Hartman, 1954), of little use in the 

present context. 
Interest in the relation between the decline of 

fishery resources and the deterioration of water 

quality in San Francisco Bay was not formally 

renewed until 40 years later, in the early 1950's, 

when Filice (1954a and b, 1958, 1959) investigated the effects of domestic and industrial waste 

on the composition and abundance of benthic 

organisms. Filice's study was based on sampling 

at 460 stations along the south margin of the 

waterway between Point San Pablo and the 

Antioch Bridge between April 1951 and April 

1952. A small Ekman grab (Ekman, 1911} was 

used for sampling by hand in shallow water and 

a larger Petersen grab (Petersen, 1911) for deep 

water (neither of these samplers bites as deeply 

into the sediment as the orangepeel grab used in 

the Albatross Expedition). In addition to numbers 

of species and specimens, Filice measured biovolume, the volume of water displaced by preserved specimens. He observed that biovolume 

was lowest in sandy sediment and highest in 

gravel-rocky sediment, but he realized that such 

distributions were also related to salinity and 

proximity to waste outfalls, precluding the determination of true sediment preferences of most 

species on the basis of parameters measured. 

Filice observed that industrial wastes were significantly more toxic than domestic wastes, for the 

fewest numbers of species and specimens were 

found at industrial outfalls and numbers increased 

with distance from the outfalls. A few more 

species were tolerant of domestic sewage at its 

source, but downstream a number of species were 

found in great abundance, apparently thriving on 

the organic matter from domestic sewage that provided a plentiful food source when diluted and 

adsorbed onto sediment particles. This was not so 

in areas marginal to industrial outfalls. That discharge of fresh water alone can have detrimental 

effects on estuarine organisms was disregarded as 

a possible reason for the scarcity of organisms 

near outfalls. 

Filice concluded that because species distributions and abundances were somewhat similar to 

those reported from the Albatross Expedition 

(Packard, 1918a and b), whereas the samplers 

used and locations examined were different, there 

was little evidence of faunal change since the 

Albatross study. 

At about the time (1953} of Filice's study, the 

engineering firm of Brown and Caldwell (San 

Francisco) was retained by the City of San Jose 

4 

to survey the effects of untreated waste entering 

the south end of San Francisco Bay from Coyote 

Creek. In addition to samples for the chemical 

analysis of water and sewage collected five times 

during the year, samples for a description of the 

number and kinds of benthic invertebrates were 

collected in October 1953 at 27 stations in the 

area south of the Dumbarton Bridge with an 

Ekman grab and cursorily examined by the California Department of Fish and Game (Brown and 

Caldwell Engineers, 1954). Although the data on 

benthic organisms were limited, the scarcity of 

animals in Coyote Creek above Gray Goose Slough 

was suggested as evidence of a toxic environment. 

With this modest undertaking, the study of the 

benthos of San Francisco Bay became the interest 

of local governments around the bay and signaled 

the beginning of public concern about short- and 

long-term effects of unregulated disposal of waste 

into the bay. Studies commissioned by these governments to determine the effects of local waste 

discharge have been conducted to the present. 

A survey of the physical and chemical conditions of the bay bottom and associated benthos 

off Point Richmond was conducted in 1953 by 

M. L. Jones under the direction of the California 

Department of Fish and Game (California Department of Public Health, 1954). The study was 

intended as a baseline investigation prior· to the 

operation of a sewage outfall in the area. Sixty-five 

stations were occupied during September 1953, 

and subsamples of those animals collected in a 

single Ekman grab sample per station were identified and counted. Physical and chemical factors 

associated with the water and sediments were 

measured at 25 of the stations. Because of the 

lack of replicate samples (by which one can judge 

how representative a single sample might be) and 

the few environmental and pollution parameters 

measured, the report could conclude only that 

waste discharge had little noticeable effect on the 

benthos near Point Richmond. Jones recommended that replicate samples be collected and 

that more physical and chemical factors be considered in future studies. 

Jones resumed the Point Richmond survey in 

1955 and 1956 (Jones, 1961). He was concerned 

not with pollution effects but with determining the 

effect of variations in sample size and number 

upon estimates of the dispersion characteristics of 

species populations. Jones studied the spatial distributions and life histories of the important 
species at four stations in the vicinity of Point 

Richmond by collecting 30 replicate core (glass 

tube, outside diameter==22 mm) samples and one 

Ekman grab sample at each station on 10 occasions between January 1955 and March 1956. 

Because of the small size of the core sampler used, 

the number of specimens recovered per species 

was in most cases very small. Nonetheless, Jones 

showed that some species were distributed as separate clumps of specimens, not randomly distributed as must be assumed when only one sample 

per station is taken. He confirmed that multiple 

samples of small size are preferable to single large 

samples when quantitative population data are to 

be interpreted correctly. Jones' work provides 

valuable details on seasonal changes in specimen 

size and abundance of some of the smaller species 

in the Point Richmond area. 

In the following year, 1957, the California 

Department of Fish and Game examined the 

benthos of the bay region south of the Dumbarton 

Bridge to evaluate the effects of sewage effluent on 

fish, benthic invertebrates, and water quality during the canning season (Pintler, 1958). One 

sample was taken with an Ekman grab at each of 

24 stations in September 1957. The animals and 

plants were sorted into major taxonomic groups, 

counted, and measured by volume. A total of 22 

groups ("organisms") were identified in all 

samples, but only in a few cases did these groups 

represent individual species. The study attempted 

to relate the level of pollution, as defined by turbidity and oxygen concentration, to the number of 

kinds of organisms and biovolume at a given location. On this basis three zones were seen: the 

headwaters of the sloughs, where few or no "organisms" existed; the mouth of Coyote Creek, where 

a limited variety was found; and Mowry Slough, 

where bottom life was diverse in terms of number 

of different kinds of animals. The report suggested 

that the first two areas were in an "unhealthy" 

condition. The highest productivity (biovolume) 

occurred in the area of "recovery" at the mouth of 

Coyote Creek, in agreement with the findings 

reported by Filice (1954) of similar conditions in 

a creek (Castro Creek) near Point San Pablo; that 

is, a few species thrived in the zone downstream 

from the source of organic pollutants. Comparison 

with the 1953 data from the same area (Brown 

and Caldwell Engineers, 1954) was not possible 

because of differences in sampling locations and 

methods of faunal identification, although a simi5 

lar lack of benthic animals in the upper reaches 

of Coyote Creek and the other sloughs was noted. 

The most extensive study of the benthos of San 

Francisco Bay was conducted by the Sanitary 

Engineering Research Laboratory (SERL) of the 

University of California at Berkeley. This investigation (henceforth referred to as the SEF.Lstudy) 

was carried out as part of an investigation "of the 

possible adverse effects of water pollution on the 

water quality characteristics and th~ fishery 

resources of San Francisco Bay" (from preface to 

Jenkins and others, 1965). Begun in ~.958 as a 

pilot study of the bay south of the Dumbarton 

Bridge (Harris and others, 1961), the study 

eventually encompassed the entire bay as far 

north as the Antioch Bridge, with sampling every 

2 months until June 1964. The findings were 

reported in four annual reports and eight final 

reports to the California State Water Pollution 

Control Board (as cited in Pearson and others, 

1970). This study provides the most data on San 

Francisco Bay invertebrates. Because of difficulties 

in methodology (both in sampling and species 

identifications), however, specimen counts and 

biovolume data must be considered qualitative 

and used with great caution in comparing with 

data of subsequent benthic surveys. 

The results of the SERL study sugge:1t, in concurrence with Packard's findings (1918a, b), that 

in species composition benthic asseml'lages are 

roughly similar throughout most of the bay 

between the Dum barton Bridge and Carq uinez 

Strait except for the predominance cf strictly 

marine species near the Golden Gate. Different 

assemblages are found in Suisun Bay l'~cause of 

the depressive effect of brackish water on the 

number of species and below Dumbarton Bridge 

presumably because of the toxic effect. of waste 

discharges that are little diluted in th~ shallow, 

restricted water. Similar conclusions were reached 

by Brinkhurst and Simmons (1968) aft~~r some of 

the oligochaetes (fresh- or brackish-water segmented worms) collected in the SERL ftudy during 1961 and 1962 were reidentified. 

The data from the SERL study were later used 

(Storrs, Pearson, Ludwig, Walsh, and Stann, 

1969) to further investigate the relations between 

physical and chemical parameters of the water 

and sediment and species diversity ( tr~ number 

of kinds of organisms) found at different locations 

in the bay. Using a diversity index der~ved from 

information theory (see section "Effect of Poilu-
tants on Benthic Animals-the Diversity Index") 

species diversity was computed for all samples 

taken in the SERL study. It was found that water 

chlorosity (salinity) and sand content of the sediment accounted for most of the variation in diversity among stations (median values per station 

were used in this analysis, that is all data from one 

station lumped) and that diversity generally 

decreased with distance from the mouth of the 

bay toward the northern and southern extremities 

of the bay. Lower-than-predicted values of diversity at stations near waste outfalls, especially in 

the south bay, the region below the San FranciscoOakland Bay Bridge, led to the suggestion that 

the diversity index might be a valuable tool in 

assessing the toxicity level of the environment. 

The inappropriateness of this suggestion is discussed in the section on diversity indices. 

The species composition of the benthic fauna 

of the San Francisco waterfront was determined 

from samples collected by Dederian ( 1966) 

between Rincon Point and Point A visadero within 

1,000 meters of the shoreline. In fall and winter of 

1961, Dederian collected single samples at 147 

stations with a "modified" Petersen grab from 

which all organisms were identified (after removal 

of 500 cm3 of sediment for particle-size analysis) and the distribution of individual species 

described. His study provides useful information 

on the relative abundance and sediment preference of the most common species. Dederian suggested, from comparisons with the work of Filice 

( 1958) and Jones ( 1961), that the San Francisco 

waterfront supported the richest fauna (numbers 

of species and biovolume) in the estuary. He 

could not, however, give precise reasons for this 

finding. 

In 1963, as part of a 3-year biological survey of 

San Francisco Bay by the Marine Resources Operations Laboratory of the California Department of 

Fish and Game, benthic samples were collected 

monthly at six stations between Richmond and 

a location south of the Dumbarton Bridge (Aplin, 

1967). At each, one sample was collected with a 

small orangepeel grab, and the contained species 

identified, counted and measured, and the seasonal abundance of dominant species for each 

station noted. The value of benthic invertebrates 

as a resource was stressed in this report, but no 

comparisons between this and previous studies 

were made. 

6 

In 1961 the Delta Fish and Wildlife Protection 

Study (Kelley, 1966) was organized to investigate 

the effects of future water development on the 

fauna of the Sacramento-San J oaqui1. River estuary. As part of this investigation, th~ benthos of 

the San Pablo and Suisun Bay area was investigated in 1963 (Painter, 1966). T·vo or three 

Petersen grab samples were collected monthly at 

each of 27 stations arranged in eight transects. All 

animals were counted identified, ard their volumes determined. Sediment particle size and 

cholorinity (salinity) were roughly determined. In 

examining the relations between the distribution 

of 11 of the 40 species recognized and bottom type, 

depth, and chlorinity, it was found that the effects 

of sediment and depth were difficult to differentiate and that the chlorinity regime (low concentrations in Suisun Bay, higher in San Pablo Bay) 

seemed to be dominant in regulating the distribution of many of the species. This coincides with 

the findings of all previous workers (for example, 

the faunal break at Carquinez Strait described by 

Filice, 1958). Seasonal fluctuationr in species 

abundances were observed, but relathns between 

mean animal size and abundance (that is, descriptions of life histories of these species) were not 

determined. 

Bottom-sediment samples collectei by Moore 

(1965) in June 1964 at 50 stations jus~ outside the 

Golden Gate in a study of sediment transport on 

the central California continental shelf were used 

to describe faunal communities of the area (Yancey and Wilde, 1970). These samples, collected 

with a pipe dredge (a pipe opened at one end that 

is dragged along the bottom to scour rurface sediments), were dried and stored for several years 

prior to the examination of the fauna contained. 

Yancey and Wilde screened the driec1 samples to 

separate the remaining hard parts of the benthic 

organisms. They identified these hari parts and 

attempted to estimate and compare tl'~ biological 

"productivity" (the percentage by weight of hard 

parts in each sample) of the stations. The loss of 

soft-bodied organisms was not considered critical 

to the outcome of this study, although in the adjacent area of central San Francisco Bay, the SERL 

study found that soft-bodied organis1ns made up 

55 percent of the total number of spe~ies (Storrs 

and others, 1965, table 6-4, p. VI-6, 7). Moreover, 

whether the mollusks were living or dead at the 

time of collection apparently was disregarded. 
Because of these limitations and omissions, the 

descriptions of faunal communities and comparisons of their levels of productivity are virtually 

useless. Nevertheless, these data were presented 

as part of a more recent study of the ecological 

conditions of the area outside the bay as these 

conditions relate to waste disposal (Brown and 

Caldwell Engineers, 1971). 

Vassallo (1969a, 1971), in May and June of 

1967, collected benthic samples on an intertidal 

mudflat on the east side of San Francisco Bay just 

north of the San Mateo Bridge, using a reinforced 

%-gallon milk carton as a sampling device (Vassallo, 1969b) to collect one sample at each of 63 

stations along three 700-m transects extending 

outward from the shoreline. Her reports describe 

the distribution of several of the dominant species 

with regard to tide level and water currents, as 

well as the vertical distribution of the organisms 

within the sediment, and conclude that distribution of the dominant species on the mudflat 

resulted at least in part from competition and food 

availability. The effects of man are not mentioned. 

To evaluate short- and long-term effects of 

dredging and spoils disposal associated with maintenance of the ship channel of north San Francisco 

and San Pablo Bays (preliminary investigations 

pertaining to the U.S. Army Corps of Engineers' 

John F. Baldwin Navigation Channel Project), 

personnel at the Tiburon Marine Laboratory 

examined the demersal (bottom-living) fish and 

invertebrate fauna of the area (U.S. Fish and 

Wildlife Service, 1970). Seventeen stations were 

visited monthly between September 1967 and 

August 1969. Benthic invertebrates, however, were 

not collected until January 1968 at 12 of the stations, and later at the five remaining stations. The 

stations were selected to include dredged areas, 

disposal areas, unspoiled or nondredged areas, as 

well as shallow and deep areas. Laboratory studies 

were made to determine the gross effects of turbidity on certain fishes. The method of collection of 

benthic animals was unspecified, but all organisms 

(other than polychaetes and small gastropods) 

larger than 0.5 millimeters were counted and identified. These investigators could find no significant 

differences in number of species between the 

dredged and nondredged deep stations but indicated that there were more species at the deep 

stations than at the shallow ones. The omission of 

polychaetes from the analyses is unfortunate, as 

7 

these organisms were shown in the SERL study to 

make up nearly half of the species ir the San 

Pablo area (Storrs and others, 1964). Nonetheless, species diversity was computed, as for the 

SERL data, for each season at each st£tion. The 

Fish and Wildlife Service found the same trends 

in diversity associated with depth and ralinity as 

previous workers but was unable to show significant differences between spoil and nonspoil areas. 

It did report that at two stations near Marin 

Island spoils disposal significantly reduced the 

number of specimens and species, and recovery 

over the next 14 months was slow. At two other 

spoil sites near the ship channel in San Fabio Bay, 

no effects were observed. It was suggested that 

significant effects of spoils disposal on biological 

populations are short termed (less than 6 years) 

and vary with method of dredging anc1 disposal, 

geographic location, depth, and season. The omission of the polychaete and gastropod data may 

affect the validity of these conclusions. 

Public demand for better water qual~ty in San 

Francisco Bay resulted in authorization by the 

State Legislature in 1965 of the San Francisco 

Bay-Delta Water Quality Control Program. 

Coordinated by Kaiser Engineers (Oakland), this 

program was established to determine the effects 

of waste collection and disposal and to develop 

plans for the control of water pollution (Kaiser 

Engineers, 1969). In addition to reviews of existing data regarding benthic invertebrates of the 

bay (Kaiser Engineers, 1968a; California Department of Fish and Game, 1968), thir program 

incorporated an investigation of the diversity of 

the benthic fauna at stations throughout the bay 

for comparison with the data of the earlier SERL 

study (Kaiser Engineers, 1968b). In March 1968, 

two to four samples were taken at each of 20 stations with a small orangepeel dredge for computation of animal numbers, biovolumes, and diversity 

indices. Despite differences in sampling and subsampling procedures and the fact that the 1968 

data represented only one point in tine, Kaiser 

Engineers considered the diversity datr.,. from the 

two studies to be comparable. The dat.,. from the 

1968 survey revealed trends similar to those 

reported in the SERL study (lower diversity away 

from the bay mouth toward the north rnd south) 

with similar values in all but the south l'q.ys where 

the 1968 diversity values were somewhat lower. 

Kaiser Engineers ( 1969) concluded that diversity 
had decreased significantly in the south bay in the 

intervening years. By implication, the continued 

introduction of toxic substances was suggested as 

the primary cause of the decrease. 

Another survey of the Coyote Creek area was 

undertaken by Allen (1971) to determine whether 

the benthic fauna had changed since the SERL 

study of the same area in 1961 and 1962. Using 

an Ekman grab, Allen collected replicate samples 

at 12 stations (with two exceptions, in Coyote 

Creek or its tributaries) in a preliminary survey 

conducted between March and June 1970 and at 

11 stations (all in Coyote Creek or tributaries) in 

the main survey conducted between September 

1970 and February 1971. Presumably because of 

the coarseness of the screen upon which the 

samples were washed, Allen found only 14 species 

or faunal groups. He measured biovolume and 

determined diversity from his species and specimen count data using the formula 

d== (S -1) /InN, 

where dis the index of diversity, S the number of 

species, and N the total number of specimens. 

After recomputing species diversity for the SERL 

data (less the data concerning faunal groups not 

found in the later study) using the preceding formula, Allen compared by station the two sets of 

biovolume and diversity data. He concluded that 

biovolume had increased at some locations since 

the 1961-62 study but that diversity had not 

changed in the Coyote Creek area in the 10 years 

between studies. 

In 1969 the City of San Francisco engaged the 

engineering firm of Brown and Caldwell to make 

necessary investigations into the design and location of submarine waste outfalls in order that the 

city might comply with State and Federal water 

quality regulations. Ecologic conditions in the 

marine environment adjacent to the City of San 

Francisco (Brown and Caldwell Engineers, 1971) 

were a part of the study. Of most concern were the 

proposed disposal sites in the channel between the 

City of San Francisco and Alcatraz Island and on 

the continental shelf seaward of the Golden Gate 

(Gulf of the Farallones). Between April and October 1970, five stations were visited in each of the 

two areas. At least two samples were collected 

(and combined) at each station with a Petersen 

or an orangepeel grab, and the contained organisms generally identified only to phylum or family. 

Most of the benthic data presented in the final 

8 

report were reprinted from species li~ts reported 

by Yancey and Wilde (1970) (described previously). Despite the crudeness and omissions of the 

two sets of data, four faunal communities were 

described: shelf, near reef, bar, and bay communities, distinguished by bottom-sediment type and 

exposure to wave action and current. The comparisons of biological productivity, because they 

were based principally on the dried samples 

described by Yancey and Wilde ( 1970), have little 

validity. The comparison of species diversity estimates for each community type is equally 

questionable because species identifications were 

incomplete. 

Included in the Brown and Caldwdl investigation were field studies in which divers made qualitative and semiquantitative observations of the 

large dominant forms of fauna at locations along 

nearshore transects and intertidal E.reas in the 

vicinity of the Golden Gate. The most useful contribution of the biological studies associated with 

this project was the laboratory investigation into 

survival rates of selected planktonic and benthic 

invertebrates subjected to varying dilutions of 

domestic waste. This study revealed tb:tt at higher 

concentrations (dilution ratio of effl·1ent to sea 

water less than 1 :20) waste materialr could alter 

or stop normal biologic processes witl·in 96 hours 

of initial exposure. These results can not be considered definitive, however, because the workers 

failed to demonstrate clearly that specimen 

handling and experimental method ole ~y were not 

responsible for at least some of th~ mortality 

(especially with regard to the larval invertebrate 

experiments). This failure prevents proper interpretation of differences between experimental and 

control tests. Additionally, the most realistic 

experiments, the continuous flow bioassays, did 

not include study of organisms found at the specific disposal sites, nor were the expo.riments- of 

sufficient duration to measure true tox~~ity effects. 

Nonetheless, the conclusion drawn from all biological investigations in the Brown and Caldwell 

study (but based primarily on the lab·uatory bioassay studies) was that the biota would not be 

adversely affected by waste discharge given proper 

location of outfalls and dilution of waFt~ material. 

To obtain a more quantitative assessment of 

the depressive effects of toxic substan~es in waste 

discharges, the State Water Resour,~es Control 

Board began a more detailed study in 1970 (California Water Resources Control Board, 1972a). 
Six restricted areas, waste dispersion zones in 

proximity to waste outfalls, were selected around 

the bay for a detailed comparison of toxicity levels 

and benthic diversity. Four replicate samples were 

collected with a Ponar grab (Powers and Robertson, 1967) at 8-14 stations within each area on 

one or two occasions between September 1970 and 

April1971, and species diversity of the contained 

specimens correlated with the level of toxicity 

(biological oxygen demand and concentrations of 

suspended solids, grease and oil) of receiving 

waters. In general, species diversity decreased 

with increasing toxicity within each area. Again, 

it was reported that diversity had decreased since 

the SERL study, but this conclusion was considered tentative because of the differences in 

sampling techniques used. 

Burton ( 1972) examined the relation between 

the sulfide content of sediments and the diversity 

of benthic organisms south of the Dumbarton 

Bridge. He took five Ekman grab samples between 

July and September 1971 at each of 45 stations 

throughout the region, including the shallow mudflats not normally sampled in benthic surveys. 

One-liter subsamples were taken from each grab 

sample, the animals identified and counted, and 

diversity computed as in previous studies. Additional sediment samples were collected for the 

analysis of sulfides. Thirty species were identified 

in this study, six more than found by the SERL 

study for the same area, but there was little evidence of a faunal change since the earlier study. 

The abundance of organisms was greater and the 

point of maximum specimen abundance had 

apparently moved southward to a point near the 

mouth of Coyote Creek. Burton suggested, contrary to the conclusions of the San Francisco BayDelta Water Quality Program report (Kaiser 

Engineers, 1969), that as abundance and diversity 

had increased near Coyote Creek, toxicity had 

decreased in the area. Burton found a positive correlation between species diversity and sediment 

sulfide content, in contradiction to that predicted 

by Storrs, Pearson, Ludwig, Walsh, and Stann 

( 1969) , the highest values of both parameters 

measured being along the shallow west margin of 

the bay near Palo Alto. 

Other small-scale regional studies of benthic 

organisms, conducted primarily by engineering 

firms under contract to various municipal and 

private organizations, are being made to assess the 

effects of domestic and industrial waste disposal 

9 

on water quality and marine life. Mort. are concerned with actual or potential changes in the 

diversity of the biota associated with increased 

toxicity of the water for comparison with the data 

from previous investigations (for exarr.ple, Jenks 

and Adamson Engineers, 1971). The problems 

inherent in such comparative studies are discussed 

subsequently. 

SUMMARY 

The results of 60 years of benthic sampling, 

despite varying capabilities of workers involved, 

differences in methods used, and diversity of objectives sought, reveal basic patterns in th~ distribution and abundance of organisms livng at the 

bottom of San Francisco Bay. A diver,:;-e, strictly 

marine fauna similar to that found 0:'1 the continental shelf of central California extenis through 

the Golden Gate into the deeper, central part of 

the bay (the area east of the Golden Gate to Angel 

and Treasure Islands, including the narrow passage to the north of Angel Island). Be~ause they 

are dependent on high salinity and lovr temperatures, these species are not found in the shallower 

reaches of the bay. At the extreme ends of the bay, 

a meager fresh- or brackish-water fauna exists, 

restricted to the river and stream inlets because 

of its affinity to fresh water. Between Carquinez 

Strait to the north and below Dumbar~on Bridge 

to the south is a fauna composed of organisms with 

a tolerance for wide fluctuations in te'llperature 

and salinity. These species population!! are maintained in the estuary by water circulation patterns 

characteristic of all estuaries (Carriker, 1967; 

McCulloch and others, 1970); they belong to 

genera that are found in most estua1..;es of the 

world. Much evidence indicates that this is at least 

in part the result of intentional or accidental introduction of many of these species into the bay by 

man (James T. Carlton, California Academy of 

Sciences, oral commun., 1972). Durin'! the past 

125 years, for example, the importation of oyster 

populations and the dumping of ship ballast into 

the bay provided the means by which numerous 

species were transported from estuari ~s around 

the world to San Francisco Bay. These species 

thrive in the bay but are often not found outside 

the bay on the open coast of Californk. 

Within the major faunal groups determined by 

salinity are subgroups composed of organisms 

with specific depth and sediment preferences: 

Species that are found most commonly in intertidal or shallow subtidal mudflats at tl-a. margins 
of the bay, or in the deep muds, sands, or gravels 

of the channels and bars. Packard ( 1918a and b) 

and the authors of the SERL study (Storrs and 

others, 1966b) found that faunal assemblages at 

stations between Carquinez Strait and the Dumbarton Bridge having similar depth and sediment 

characteristics contained many of the same 

species. The actual constitution of the assemblage 

at any location, however, is distinct because of the 

extremely variable combinations of local physical, 

chemical, and biological factors. It is the relation 

between local benthic-community structure and 

naturally occurring environmental factors that 

many of the workers attempted to define (Packard, 1918a, b; California Department of Public 

Health, 1954; Filice, 1958; Jones, 1961; Dederian, 

1966; Painter, 1966; Aplin, 1967; Vassallo, 1969a, 

1971). These workers made little or no attempt to 

describe recent changes in the communities studied, but instead accepted the patterns in their 

observations as reflecting natural (cyclical or 

steady-state) phenomena. Their studies were too 

discontinuous in both time and space to provide a 

cohesive picture of the structure and function of 

the entire benthic community of San Francisco 

Bay, but they do provide generally reliable qualitative descriptions of the major components of the 

fauna and the associated physical and chemical 

environments. 

The normal benthic assemblages described are 

altered by the usually depressive effects of man's 

waste disposal first noted in the bay by Filice 

( 1954a); many species are eliminated because they 

are unable to tolerate a polluted environment. In 

areas subjected to concentrated wastes, a few 

tolerant species survive and, in the absence of 

competition for food and space, thrive in great 

numbers (Filice, 1959), depending on the type 

and dilution rate of the waste material. A short 

distance away from the source of waste material, 

however, changes in normal biologic processes 

brought about by changes in the physicochemical 

environment (for example, increased toxicity of~ 

the water) are difficult to recognize and measure. 

Nevertheless, in appraising man's impact on the 

environment of large areas, authors of pollutionoriented studies have often interpreted their observations in terms of pollution effects, and volumes 

of data on the San Francisco Bay estuary have 

resulted from efforts to quantify these observations, primarily by relating the diversity of organisms to specific criteria for water or sediment 

10 

quality (Storrs and others, 1966b; Kaiser Engineers, 1968b; U.S. Fish and Wildlife SE-rvice, 1970; 

Burton, 1972; California Water Resour~es Control 

Board, 1972a). Unfortunately, we still understand 

little of the precise physiological mech~.nisms that 

maintain these patterns; that is, how water quality 

or sediment characteristics affect individual 

organisms. But, all the surveys provide information useful in formulating research projects 

designed to help define these mechanisms. For 

instance, from the species lists provided in the 

reports of the SERL study (see Storrs and others, 

1966b), we can choose those species t':lat because 

of their size or abundance might be best suited to 

detailed studies of population biology, that is life 

histories, rates of birth, growth, and mortality, 

and mechanisms and rates of the uptake and 

release of pollutants. The data we novr have allow 

us to predict where these species migl't be found; 

further study presumably will reveal the reasons 

for nonpredictable distributions. 

However, despite the extensive sampling of the 

benthos of San Francisco Bay and the publication 

of the numerous reports described h~rein, there 

are actually few reliable quantitative data on the 

numerical abundance and biomass di~tribution of 

the benthic fauna with which future data might be 

compared. Quantitative baseline data, collected 

with rigorous attention to reproducible sampling 

methodology and data analysis, are necessary if 

we are to detect changes in the species composition of benthic communities and to relate these 

changes in a cause-effect manner to changes in 

water quality. 

Methods for the collection and processing of 

samples have varied widely from surw~y to survey 

and generally also have been nonquantitative; in 

addition, species identifications have been in many 

cases incomplete or erroneous, and data analysis 

and interpretation, without exceptior ~ have been 

limited by lack of precision and statistical validation. Further, because the samples from many 

of the earlier studies were not retained (James T. 

Carlton, California Academy of Sciences, oral 

commun., 1972), reanalysis of those data is impossible. As Hedgpeth (1969, p. 384) commented, 

"The critical, comprehensive study of the benthos 

of San Francisco Bay * * * still re:'llains to be 

done." An understanding of the limitations of past 

benthic investigations is important if future 

studies are to provide the information necessary for assessing man's impact on th~ estuary. 
INADEQUACIES OF EXISTING DATA 

SAMPLING METHODOLOGY 

Quantitative benthic sampling methods were 

developed in Europe more than 60 years ago when 

the need arose for estimating, on an areal basis, 

the potential food supplies of fish populations 

(Petersen, 1913). Devices that collect bottom 

samples of known dimensions (for example, 0.1, 

0.2, or 0.5 m2 ) have been used since that time 

(Thorson, 1957), and data collected worldwide 

are comparable on that basis. Sampling of the 

benthos of San Francisco Bay has bee11 done with 

little regard for such standardization (table 1), 

as exemplified by the change of methoc ~logy durTABLE 1.-Summary of methods used in surveys of the benthic organisms of San Francisco Bay, arr':l.nged alphabetically by author 

Reference 

Number of stations; 

number of samples at each station 

Sampler 

(area) 

Screen 

mesh size (mm) Count data Identification level Biomass 

estimate 

Allen (1971) ---------------- 23;3-7 .................... Ekman 1.5 All species .............. All species .............. Biovolume 

(-0.02 m 2 ). of species. 

Aplin (1967) ................ 6;1 ........................ 100 in. 3 orange- Not given All but Dominant None. 

Brown and Caldwell 

Engineers 

(1954). 

Brown and Caldwell 

Engineers 

(1971). 

Burton (1972 ) 

California 

Department of Public Health (1954). 

California Water Resources Control Board (1972a). 

Dederian (1966) 

Filice (1954a, 

b, 1958, 

1959). 

Jones (1961) ............... . 

Kaiser Engineers 

(1968b). 

Packard (1918b) 

Painter ( 1966) ........... . 

peel (-0.07 m2). small species. 

organisms . 

27;1 Ekman .............. do .............. None ........................ Faunal types Do. (-0.02 m2 ). (crude). 

10;2, 

samples 

combined. 

Petersen .............. do .............. All species .............. All species ............. . Do. (0.5 m2 ) or orangepeel (?) . 

45;5 ........................ Ekman (-0.02 m 2 ). 

65;1 ...................................... do ....................... . 

6 areas, 8-14 stations per area; 4. 

6.4-1 Ponar (-0.05 m2 ). 

147;1 ........................ Petersen 

460;3, 

samples 

combined 

(shallow). 

(-0.1 m 2 ). 

Ekman (-0.02 m2 ). 

1 (deep) . _______ Petersen (?) ................... . 

4;30 ...................... 22-mm corer (-3 cm2 ). 

4;1 ........................ Ekman 

20;2-4, 

samples 

combined and inconsistently 

subsampled. 

27;1 or 2 ............... . 

(-0.02 m 2 ). 

100 in.a orange- peel (-0.07 m2 ). 

2.5 ft3 orange- peel (-0.7 m 2 ). 

27;2 or 3 ................ Petersen (-0.09 m 2 ). 

1.0 

.42 

.6 

1.6 

. ....................... do ............................ do 

All large; 

subsamples 

of small. 

do 

All species .............. .............. do 

Do. 

Biovolume of species. 

Dry weight of species. 

do .............. .............. do .............. Biovolume of total sample. 

do .............. .............. do Do. 

-1.0 ......................... do ............................. do .............. Do. 

.417 All species .............. All species .............. Biovolume of species. 

.417 .......... ·············· do ···························· do ·····-······-- no. 

.5 

.6or 

.3 

All species 

in 

subsamples. 

All large; 

subsamples 

of small. 

All species 

in 

subsamples 

All species 

of mollusca. 

Biovolume of phyla. 

NonE". 

All species .............. All species .............. Biovolume of sel·~cted species. 

Pintler (1958) ............ 24;1 ........................ Ekman (-0.02 m2 ). .6 Major faunal "components." 

Major faunal "components." NonE". 

Storrs, Pearson, and Selleck 

(1966a). 

U.S. Fish and Wildlife Service 

(1970). 

Vassallo 

(1969a, 

1971). 

Yancey and Wilde ( 1970). 

[1958-59] 

10;2. 

[1960-61] 

28;2. 

[1961-62] 

28;2. 

[1962-63] 

29;2, samples 

halved and combined. 

[1963-64] 

18;2, samples 

halved and combined. 

100 in.3 orange- peel (-0.07 m2 ). 

do ....................... . 

do ....................... . 

220 in.a orange- peel ( ?) ; 300 in.3 

Petersen 

(0.065 m2 ) for sand stations. 

.............. do ........................... . 

17; (?) .................... Not specified ................... . 

63;1 

50;1 

Box corer (94 cm2 ). 

Pipe dredge ..................... . 

1.3 All species 

sample data combined. 

All species .............. Biovolume 

........................ do ............................ do 

. ....................... do ............................ do 

.5 All species .............. ... ......... .. do 

do .............. .............. do .............. .............. do ............. . 

.5 

.297 or .500 

.5 

All species 

except 

polychaetes 

and small gastropods. 

All large; 

subsamples 

of small. 

All hard 

parts. 

All species 

except 

polychaetes 

and small gastropods. 

All species ............. . 

All hard 

parts. 

of species. 

no . 

no. 

no. 

no. 

Non£. 

Non£. 

Dry weight. 

11 
ing the course of the SERL study, in which two 

sizes of orangepeel grab and a Petersen grab 

and at least two sizes of screen mesh for separa ting animals from the sediment were used on different occasions. Without proper attention to 

sampling methodology and standardization, possible changes in the composition of faunal assemblages between surveys go undetected. 

Unfortunately, samples obtained during the 

first major benthic survey in the bay, the Albatross Expedition, were collected with the roughly 

circular, but nonquantitative, orangepeel bucket 

sampler; its use undoubtedly influenced later 

workers in their choice of sampler. (See, for 

example, Harris and others, 1961.) Thorson 

( 1957) pointed out that this sampler was designed 

primarily for retrieving submerged pipes and caissons and for reconnaissance work and was not 

suitable for sampling that would make possible a 

critical evaluation of the distribution of benthic 

fauna. The orangepeel grab collects variable 

amounts of sediment, depending on substrate 

hardness (a fact recognized by the participants of 

the SERL study midway in their program), and 

it may overflow and be subject to washing action 

as it is brought to the surface, causing loss of the 

surface sediments and the associated fauna. Yet 

its use is still recommended for surveys of benthic 

fauna (American Public Health Association and 

others, 1971,p. 764). 

The small Ekman grab and hand corers, convenient for intertidal or shallow-water sampling 

from a small skiff, provide a sample generally too 

small for statistical comparison with the data 

obtained with more conventional large deepwater 

samplers, especially a comparison of data concerning the larger, more widely dispersed animals. The 

small samplers do retrieve without loss quantitative samples that can be compared with other 

samples of similar size. 

Because the area sampled by the grab commonly was not known, data from different surveys 

could not be normalized and compared on that 

basis. Abundance and biomass were most commonly expressed as functions of volume of sediment sampled, despite evidence that depth (and 

volume) sampled varied with sediment hardness. 

This is especially critical when one considers that 

most organisms live on or near the sediment surface; that is, the number of organisms found does 

not necessarily increase with depth of sediment 

sampled. Estimates of volume of sediment 

12 

sampled, therefore, have little meaning in comparing samples from regions of different sediment 

types. 

The need for replicate samples in biological 

investigations has been well demonstrated (Jones, 

1961; Storrs and others, 1966a; Lie, 1968), not 

only for use in statistical analyses of sampling 

error and patterns of animal distributions but also 

to obtain complete lists of species pres:mt. Ideally 

the number of samples to be collected is based on 

the size and dispersion patterns of the animal 

populations to be studied as determined from a 

reconnaissance survey. In studies of the benthic 

fauna of San Francisco Bay, the number of 

samples taken at each location and sampling period varied (generally only one or two samples per 

station), and the number taken was determined, 

apparently, by the amount of time (and cost) 

required to process each sample. Tha.re is some 

indication that "replicate" samples dic1 not always 

represent the same assemblage ( fc... example, 

Storrs and others, 1964), a situation that could 

arise if the survey vessels were not anchored while 

the samples were being collected. In none of the 

reports reviewed (table 1) is the use of an 

anchored vessel mentioned. In an area such as 

San Francisco Bay, where winds and tides can act 

strongly to cause ship drift, replicr.te samples 

taken minutes apart from an unancr0red vessel 

can represent widely differing habit-'lts, for the 

species composition of benthic assernblages can 

change significantly over short distz.nces where 

the sea floor is not level (Nichols, 1970). 

The size range of organisms collected is largely 

determined by the mesh size of the screen upon 

which the sample is washed. Because rlllall organisms are usually the most abundant, slight changes 

in screen mesh size will greatly affe~t the total 

number of organisms retained, if ·not the biomass 

(Reish, 1959b; Birkett and Mcintyre, 1971). Use 

of screen mesh of different sizes makes comparisons of abundance data impossible. In bay studies 

screen size has varied from the 1.6-mrn mesh used 

by Dederian (1966) to the 0.297-mm mesh used 

by Vassallo (1969a), and as menticned, screen 

size was changed several times in the SERL survey (Storrs and others, 1963). 

Filice ( 1958) observed that differences in 

sampling equipment and techniques prevent detection of changes in the composition of faunal 

assemblages between surveys. Kaise... Engineers 

(1968b) were not as cautious wher comparing 
their data with that of previous studies. Whatever the methods employed, the generally nonquantitative nature of the sampling in the bay 

(that is, inadequate equipment and improper 

sampling techniques) will make it difficult to compare past results with those of future studies. 

SPECIES IDENTIFICATIONS AND 

LIFE HISTORY STUDIES 

In checking selected samples from several of the 

major studies discussed, it has become evident 

that many of the identifications are erroneous and 

specimen counts invalid (James T. Carlton, California Academy of Sciences, oral commun., 1972). 

Improper identifications seem to result from inexperience of personnel employed as taxonomists, as 

well as from the use of highly incomplete taxonomic keys. In the only long-term study of the 

benthos of the bay, the SERL study, species identifications apparently changed from year to year; 

for example, whereas in 1960-61, 12 species or 

genera of polychaetes were recognized in the 

region south of the San Mateo Bridge, at least 21 

were recognized at the same stations in 1961-62. 

This problem is compounded by the recent introduction of species new to this part of the world 

(Hanna, 1966): many of the references commonly 

used for the identification of San Francisco Bay 

invertebrates are based on taxonomic studies conducted prior to these introductions. 

An aspect of the study of benthic animals of 

San Francisco Bay that has been neglected is that 

of the biology of the individual species themselves. 

In none of the surveys reviewed here have the 

phenomena of normal reproduction, growth, and 

mortality been considered in detail, and only a few 

of the workers considered seasonal changes in 

specimen numbers and biomass to be reflections 

of natural biological processes. 

A consequence of discontinuous sampling in 

time and space is often that natural baywide seasonal changes are interpreted as geographic differences between stations. In the reports of those 

surveys during which fixed locations were 

resampled (Jones, 1961; Painter, 1966; Storrs and 

others, 1966b; Aplin, 1967), only Jones considered 

the seasonal age structure of individual species 

populations. During any given year of the SERL 

study, only two or three of six subareas within the 

bay were studied; no single subarea was sampled 

continuously throughout the 4-year program. For 

this reason, no attempt could be made to charac13 

terize the distribution of individual species populations on a baywide basis or long-term changes 

in the species composition of faunalBssemblages 

found at each station that could provide information on the changing nature of the physicochemical environment. And no attempt was made to 

relate seasonal variability in biovolun1e with differences in the size (age) structure of the species 

populations. Only counts and total bio .. 'olumes for 

each species were computed. Other workers leave 

seasonal variations in numbers and bicmass unexplained or imply a relation to physin.al factors. 

Because of the time and effort required to measure 

the size of individual specimens, such information 

is lacking for nearly all invertebrate species in the 

bay. Jones (1961) emphasized that simple estimates of numbers of organisms, total biomass or 

biovolume, and species diversity are limited in 

value without accurate measurements of the spatial and temporal fluctuations in these parameters 

and an assessment of the dispersion pattern of each 

species relative to the size of the sa1npler used. 

Except for the study by Jones, there are no data 

of this type on the benthos of San Francisco Bay, 

and even Jones' study is limited by the very small 

size of the sampler used (that is, only a few specimens of small, abundant species were recoverable 

in the 22-mm corer) and the very small area 

studied. No truly quantitative estimate of the 

structure of the benthic community and the relation of this structure to environmental quality can 

be made until a great deal more is known about 

the normal life cycles of the organismr, 

EFFECT OF POLLUTANTS ON DEI 7HIC 

ANIMALS-THE DIVERSITY INl'~X 

The complexity of the estuarine environment 

requires that one proceed systematically in the 

study of the relation between animah and their 

habitats. Studies of the life cycle of individual 

species must be combined with measurements of 

the tolerance of these species to natural variations 

in temperature, salinity, oxygen concentration, 

depth, and sediment particle size before the consequences of water pollution can be fully determined. But it is clear that the wastes discharged 

into waterways do have disastrous effects on 

aquatic organisms; attempts to assess these effects 

are numerous. 

One commonly investigated wart,e-disposal 

problem is the effect of trace elementr and pesticides on benthic animals. Many papers report 
levels of various trace elements and pesticides in 

the tissues of plants and animals. With consistency in methodology, it is relatively easy to monitor such substances in both space and time. (See, 

for example, Butler, 1971.) There is much literature (for example, Brown and Caldwell Engineers, 

1971) reporting toxic levels of substances for individual species, usually determined as the concentration of pollutant required to kill a fixed 

percentage of test organisms within a certain 

(usually short) period. It is quite another problem to ascertain the effects of chronic low levels 

of toxic substances. 

The extent to which pollutants entering the 

marine environment are detrimental to the organisms varies greatly, depending in part on the variety and concentrations of the pollutants, the 

flushing characteristics of the receiving waters, 

and the tolerances of individual organisms. The 

relative toxicity of a given pollutant varies from 

species to species for any given concentration 

(Pringle and others, 1968; Bryan, 1971; Butler, 

1971) and for a give·n species with temperature, 

body size, and degree of starvation (Portmann, 

1968). When concentrations of pollutants are 

low, there can be uptake by some species without 

obvious detrimental effects (Butler, 1971). With 

long-term chronic exposure to pollutants, some 

species may gradually disappear from a habitat 

(regressive species), while other, more tolerant 

species replace them at the original site (transgressive species) (Leppakoski, 1968; Tulkki, 1968, 

O'Sullivan, 1971). Low, sublethal levels of some 

pollutants may affect the morphology (structure, 

color, taste, and so on), reproduction, growth, 

larval development, and behavior of certain animals without causing immediate death but lead 

to the eventual decline of the species within the 

polluted area. High concentrations of pollutants 

may cause immediate death, often the first indication that there is a pollution problem. 

While the effect of pollutants as a cause of the 

depletion of benthic animals near waste outfalls 

is generally recognized, the effect of unpolluted 

fresh water on estuarine or marine animals near 

such outfalls is commonly overlooked, primarily 

because it is difficult to distinguish. Fresh-water 

effects can be extremely severe, resulting in major 

changes in the structure of the community (Golubic, 1971). 

Field studies utilizing accurate and consistent 

sampling methodology may show a cause-effect 

14 

relation between a detected change in the environment and an unexplained change in th~ biology of 

a species or the species composition of the community. But only when the suspected factor is 

tested under laboratory conditions, '"·here other 

variables are controlled, can a relatjon be confirmed ( W aldichuk, 1969) . This complex, costly, 

and time-consuming process is now undertaken 

for only a few commercially exploited species of 

fish or shellfish (for example, Butler, 1971). Thus, 

shortcut methods for assessing the effe~ts of pollutants on the biota have great appeal where immediate answers are needed for social or economic 

problems. 

A commonly used measure of the effects of 

extreme pollution is the index of diversity. The 

index takes a number of forms, the sin1plest being 

counts of number of species and the m')st complex 

being mathematical functions of the distribution 

of specimens among species. The number of species 

usually decreases when the environment becomes 

uninhabitable for the more sensitive species 

(Wilhm, 1967; Tulkki, 1968). Near sewage outfalls, this effect is readily seen (Filice, 1954a; 

Reish, 1959a). Away from the waste s-:.urce where 

the pollutants have been diluted, tl·~ relations 

between pollutant concentrations ard. diversity 

are much more difficult to determine. 

The index used in nearly all studie~ concerned 

with diversity in San Francisco Bay is one derived 

from information theory (Margalef, 1958; Pielou, 

1967): 

in which H' is the diversity and Pi the proportion 

of number of specimens of species i to the total 

number of specimens (NJN). To use this index, 

one must count and accurately identify all species 

within the sample as well as have a dear indication of the homogeneity of samples or community 

for which diversity is measured (Mcintosh, 1967; 

Pielou, 1967). This index is affected by the 

method of collection, the identification of component groups, the size of the space sampled, and 

the population biology of the species themselves 

(Margalef, 1969). Mcintosh presented a table 

1967, table 5, p. 400) giving the mf.ximum and 

minimum values of the information-t'leory diversity index for a sample of 100 individ·.tals divided 

among varying numbers of species. For example, 

if 100 specimens are identified as representing 10 

species, the possible range of indices is 0.50-2.30, 
depending on the distribution of the specimens 

among the 10 species. If 20 species are identified, 

the range is then 1.04-2.98; if 50 species, 2.60-

3.90. The ability of the worker to distinguish similar-looking or closely-related species and to properly assign all specimens is critical to the final 

determination of diversity. Two workers with different abilities in taxonomy can easily arrive at 

quite different estimates of diversity. The chances 

for error by semiskilled workers are further compounded by the similarity of several species of 

many genera of benthic organisms at any given 

locality. 

Despite the likelihood of error in determining 

such an index of diversity, recent studies of pollution in San Francisco Bay have placed much 

emphasis on the information-theory index as a 

measure of the toxicity of the environment. In 

using data from the SERL study to relate diversity in unpolluted parts of the bay to water chlorosity (salinity) and sediment sand content, values 

lower than predicted by the chlorosity-sand relation were found in regions of suspected environmental toxicity (Storrs, Pearson, Ludwig, Walsh, 

and Stann 1969). 

Because the trends observed by Storrs, Pearson, Ludwig, Walsh, and Stann (1969, fig. 2, p. 

905) were derived from diversity data lumped by 

station over a period of 4 years without regard for 

seasonality (during which time sampling methodology and identification levels changed), the 

degree of statistical confidence around any given 

data point shown is low. The limits of confidence 

shown in their figure 2 (20th and 80th percentile 

values of diversity) indicate that 40 percent of the 

observations of diversity at each station fell outside these limits. Although the trend toward 

greater diversity near the seaward entrance of the 

bay is probably real, the overall estimates of diversity for particular locations can be accepted only 

as being very crude. Yet in a followup assessment 

of benthic diversity by Kaiser Engineers in March 

1968 as part of the San Francisco Bay-Delta 

Water Quality Control Program (Kaiser Engineers, 1968b), it was concluded that diversity had 

decreased in the southern part of the bay since 

the SERL study. This conclusion was drawn 

despite the fact that seasonal population fluctuations would be expected to reduce benthic diversity in the spring (Lie, 1968) and that the methods 

used were different (in subsampling routine) from 

those of the earlier study. In view of these compli15 

cations and the evidence that some of the species 

identifications and specimen counts reported are 

erroneous, it becomes clear that the specific conclusions of the Kaiser study relating tc decreased 

species diversity are invalid. Because no reliable 

baseline measurements of benthic diversity in San 

Francisco Bay exist, such comparisons with existing data are nearly meaningless ref'ardless of 

methods used in subsequent data colhction and 

analysis. 

As a result of the. program sponsored by the 

State Water Resources Control Board in which 

diversity indices were determined fer samples 

taken in 1970 at several locations near waste outfalls (California Water Resources Control Board, 

1972a), the Department of Fish and Game, while 

acknowledging the limitations of the c

1ata of the 

earlier studies, concluded that diversity had 

decreased since the SERL study. Again, this conclusion is not quantitatively justified whether 

there has been a change or not. Burton's opposite 

finding (1972) of increased diversity in south bay 

since the SERL study probably reflects differences in sampling methods and species identifications rather than significant faunal changes and 

serves to point up the problems inherent in such 

analyses. 

The diversity index, being sensitive to seasonal, 

spatial, and methodological variation, c':\n be used 

only as a crude tool for attempting to assess the 

"health" of an ecosystem. Only very gro~s changes 

in the physical and chemical nature of an environment as complex as an estuary can be directly correlated with diversity changes, for the statistical 

error involved in making a single ertimate of 

species diversity at one location through even a 

short time is great. Far more must be known 

about the dynamics of individual components of 

the system before this tool will be useful. Crude 

estimates of diversity similar to those dqtermined 

in the studies evaluated can be used only when 

methodology is consistent from year to year and 

normal seasonal and spatial variation"' are considered. 

PROPOSED DIRECTIONS 0~ 

FUTURE RESEARCH 

We have gained little insight into the effects of 

man on the biota of San Francisco Bay since Filice 

(1954a) observed the depression of the numbers 

and kinds of animals near waste discharges in the 

area of Point San Pablo. It is true that evidence 
gathered for the bay as a whole supports his conclusions, but we have failed to clearly demonstrate 

further deterioration of the biota (although it may 

have occurred) as a result of continued waste disposal into the bay except in the near vicinity of 

waste outfalls. More important, we do not have 

sufficiently reliable data with which future data 

might be compared. We are therefore unable to 

judge with certainty whether we have succeeded 

or failed in recent attempts to lessen man's impact 

on the biota. Nor can we decide, with the evidence 

at hand, what steps need be taken. Studies that 

will form the bases for these decisions must be 

undertaken now. 

Clearly, much of the fault of previous studies of 

the benthos of San Francisco Bay has been the 

lack of standardization and repeatability of 

sampling methods even where identification of 

genera or species may have been accurate. There 

is no single procedure to be followed in studying 

the benthos, but certain basic practices are generally accepted (see Holme and Mcintyre, 1971) 

that are statistically valid and provide ecologically relevant results. 

With a dependable quantitative grab or core 

sampler, depth and area of bite can be determined 

and there is no loss of sample during recovery. Of 

the many types of large samplers, the van Veen 

(Thorson, 1957), Ponar, and Smith-Mcintyre 

(Smith and Mcintyre, 1954) grab samplers seem 

to be the best. Lie and Pamatmat (1965) and 

Nichols (1972) have found that the van Veen is 

useful in protected waters (waters not subjected 

to deep-ocean swells, which tend to cause pretripping); it is simple to operate, and it takes a rectangular bite deep enough to collect all but the 

large, deep-dwelling forms. In certain types of 

substrate, deep-dwelling organisms may contribute more biomass than is generally the case 

(Smith and Howard, 1972); the errors inherent in 

use of the shallower samplers must be taken into 

account when summarizing count and biomass 

data. Ideally the size of the sampler depends on 

the size, abundance, and spatial distribution of 

the organisms studied. Whereas a small-diameter 

corer from which the whole sample is returned to 

the laboratory for sorting may be appropriate for 

studying small but numerically abundant amphipods or immature stages of other species of the 

bay, the grab sampler is necessary for study of the 

larger, more widely dispersed but less abundant 

species. But within a size group, methodology 

16 

must remain constant throughout the study period. Birkett and Mcintyre (1971) discussed the 

effect of varying the screen mesh size, suggesting 

that a 0.5-mm screen be used where possible. As 

it is tedious to wash a large sample over so fine a 

screen as 0.5 mm and subsequently sort large 

numbers of vary small animals under a sorting 

lens, a screen size of 1.0 mm has been more commonly used to separate the macrofauna from the 

sediment (Mare, 1942; Lie, 1968). E>naller core 

samples washed through fine screens can be use 

to collect the smaller forms in sufficif'"'lt numbers 

with considerable saving of time aboard ship 

(Nichols, 1972). This eliminates the r~ed for subsampling, a statistically questionable operation 

when done by hand aboard ship. 

The time frame of a benthic sampFng program 

must be based on the lifespan of th9 organisms 

studied if we are to obtain accurate estimates of 

the parameters of population bio10gy-birth, 

growth, and mortality rates. To separate natural 

from unnatural variations confidently, the dynamics of natural populations must b~ monitored 

for at least severallifespans (Prestor and Wood, 

1971). In addition, replicate samples need to be 

taken at each location for accurate measurement 

of sampling error and dispersion charPcteristics of 

the organisms (Elliott, 1971). 

There are numerous approaches to the study of 

benthic communities, each depending on the 

intended use of the resulting data. Or~ is to make 

an intensive areawide survey of the kinds and 

numbers of species at locations throughout the 

bay at one point in time. Through fac~or or multivariate analysis (for example, Lie and Kelley, 

1970), species composition and abundance can be 

correlated with environmental factors and the 

underlying causes for general patt,.~rns of distribution interpreted (Waldichuk, 1969). This 

approach, roughly similar in concept to that of the 

original Albatross Expedition, would provide not 

only-information regarding environmental factors, 

but also baseline data with which later similar 

surveys could be compared (using identical 

sampling techniques and at compar~.ble times of 

year). To assess the general state of "health" of 

an area such as San Francisco Bay, a baseline 

study could be compared with one made under 

similar circumstances in other bPys in lessurbanized areas. This type of comparative study 

would provide, relatively quickly, a m~asure of the 

extent of changes brought about by rrbanization. 
In view of the nonquantitative nature of existing 

data, such a baseline study remains to be made. 

Surprisingly little is known about the dynamics 

of individual species populations-normal seasonal 

and annual fluctuations in population parameters 

such as reproduction, growth, and mortality, without which little can be inferred about nonnormal 

fluctuations commonly attributed to unnatural 

environmental stresses (pollution). Detailed studies are needed at specific locations that are presumably geographically representative of larger 

areas. In order that possible relations between the 

presence of pollutants and alteration of the population parameters can be deduced and reproduced 

in the laboratory, studies in polluted locations 

(that is, near waste outfalls) should be complemented by similar studies in physically similar 

nonpolluted locations (Wass, 1967). It must be 

pointed out that there are probably no completely 

"natural" habitats left in San Francisco Bay. Comparisons with such environments require investigation of nonurbanized estuaries. Where emphasis 

is placed on the detrimental effects of pollutants, 

routine monitoring of waste discharges, bay 

water, and sediment quality through long periods 

should be accompanied by similar monitoring of 

suspected pollutants in the biota, not only by 

species, but by age (size) groups within species 

and by seasons. We need to know, for instance, 

when in the lifespan of a benthic organism it is 

most sensitive to the toxic effect of a pollutant. 

When the mechanisms and rates of uptake of pollutants by individual species have been determined in the laboratory by long-term bioassays 

designed to detect the effect of chronic low levels 

of pollutants (Tarzwell, 1971), the movement of 

these pollutants through individual species populations can be estimated and the role of the benthic ecosystem in the turnover of these substances 

delineated. 

It is worth noting here that some of the dominant species found in the bay, such as for example, 

members of the amphipod genus Corophium, 

appear to withstand polluted conditions (Fraser, 

1932; Reish, 1959a; Tulkki, 1968; Gamble, 1970). 

The usefulness of such indicator species in pollution studies has been well documented (Wass, 

1967), and the discovery of large numbers of specimens of those species known to be tolerant of 

polluted conditions is good indication that such 

conditions might exist. The study of tolerant 

species might reveal not only the mechanisms by 

17 

which they survive in a polluted envirorunent, but 

also the biochemical processes, initiated by the 

introduction of pollutants, that lead to the elimination of less-tolerant species. 

Identification of species by taxonomic specialists 

or persons trained by these specialists is critical in 

studies of the effects of water quality on a benthic 

community. Verification of the identification by 

such a specialist of a small fraction of animals collected does not insure validity of all ident:~fications. 

Improper identifications, and especially the lumping of similar species into single categori~s for the 

purposes of data analysis, lead to erron~ous conclusions about the structure and functi11n of the 

community, especially diversity of species. There 

is clear evidence that the results and conclusions 

of past benthic surveys of San Francisco Bay are 

of limited value because of such errors. After 

proper identification, the specimens should be 

stored in permanent collection, prefer~bly museums funded for the maintenance of such collections, where they can be found by interested 

persons months or years later possibly f1r reidentification, for finding attached parasit~s, or for 

determining size (age), sex, or internal structure 

of the specimens. At present, there is little regard 

for the value of such collections, and therefore 

funds and space for their storage and maintenance 

are not usually provided. 

Funds for the support of environmenta 1 research 

are normally channeled without coordination into 

many small-scale investigations, producing results 

that vary widely in quality and uqefulness. 

Benthic investigations are costly, complex, and 

timeconsuming, especially when there is need to 

draw conclusions of political or economic impact. 

Coordination not only eliminates needhss duplication but, more important, insures tl'at methodology and data reduction are compatible,. 

especially in identifying the enormous number of 

specimens that must be collected in an adequate 

assessment of the benthos of San Franciqco Bay. 

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19 

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20 

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