Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs
Authors: Amanda J Ashworth
Yichao Yang
Phillip R Owens
Lisa M Durso
Philip A Moore Jr
Cammy Willett
Kim Cook
Jennifer M DeBruyn
Journal: PeerJ (2019)
Discipline: Multidisciplinary
Keywords: Animal manure; Conservation pasture management; Microbial abundance; Soil microbiome.
Affiliations: Department of Crop, Soil, and Environmental Sciences, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America., Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America., Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, TN, United States of America., Agroecosystem Management Research Unit, United States Department of Agriculture, Agricultural Research Service, Lincoln, NE, United States of America., Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States of America., Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America, Dale Bumpers Small Farms Research Center, United States of Agriculture, Agricultural Research Service, Booneville, AR, United States of America.

Abstract:  Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha-1. Soil samples were collected at a 0-15 cm depth from 2016-2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P &lt; 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P &lt; 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health. 

Retracted: No

PubPeer comments:
 The authors never indicated in the article if their data complied with the normal distribution. Then why did they use ANOVA then? Surely most of their data had very skewed distribution curves, very far from the normal ones (the only exception might be Proteobacteria). The authors begin Discussion with u201cResults illustrate the importance for evaluating soil ecology across time and spaceu201d. How surprise here, as well as not need to perform rather extensive and expensive research to substantiate a truistic statement like this. Besides, considering the results described, one may easily conclude that there is no need at all to perform microbiome research as statistical significance does not directly translate into ecological, environmental and microbiological one (meaning the difference between treatments, even if statistically significant, is very small in terms of the real value. Then the authors continue Discussion: u201cAmong the identified dominant phyla, Actinobacteria are affected by soil moisture; considering, Acidobacteria may decrease under greater precipitation and the presence of Proteobacteria increases u201d. In Results section there was no mentioning of the soil moisture effect! Only Pasture management and zone as factors, but those are far from being 100% synonymic with soil moisture! And speaking about the dominant phyla, identified in the study, there was no Acidobacteria at all (Figure 2 and the relevant paragraph in Results section)! Thus the beginning of Discussion produces a strong impression of the text, copied from another paper, pasted in this one, but then never edited appropriately. I believe in speaks volumes both about reviewing, provided by the Journal, and authorsu2019 attitude to presenting their research. Figure 4 in the article has a caption u201c PCA of bacterial community structureu201d; however, the explanation below the caption runs as PCoA. Thus the question arises if it was principal components analysis or principle coordinates analysis. They provide the same results only in case of Euclidean distance, not B-C one. Figure 6 shows Richness (Chao) on the Y axis. But what do the values mean u2013 the number of OTUs? Or what? It is not clear from the M M or Results section. Besides, the format of the values does not seem to be correct, as there should be u201c,u201d symbol after the digit for thousand. ,