Blaire Steven

Nitrogen Fertilization Has a Stronger Effect on Soil Nitrogen-Fixing Bacterial Communities than Elevated Atmospheric CO2

ABSTRACT Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO2 and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO2 conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO2 to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil nifH composition in the three forest systems was dominated by species in the Geobacteraceae and, to a lesser extent, Alphaproteobacteria. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO2, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on nifH community structure than elevated CO2 and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO2 conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.

High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.

The extent to which different sequence-based approaches describe environmental microbial communities in comparative studies is an important consideration when deriving inferences from ecological studies. The ability of a targeted metagenomic approach [small subunit (SSU) rRNA pyrosequencing] and shotgun metagenome approaches were compared to identify distinguishing features in dryland soil microbial communities from two different habitats: biological soil crusts (biocrusts) and creosote bush root zones. A parallel comparison was conducted to determine the ability of each approach to detect community differences potentially arising from a more subtle experimental treatment, long-term elevated atmospheric carbon dioxide. As expected, the biocrust datasets were clearly differentiated from root zone datasets using either of the sequencing approaches. However, the composition described by each approach was significantly different. The magnitude of comparative differences due to habitat or elevated CO2 treatment was larger with pyrosequenced SSU datasets or SSU reads recruited from shotgun metagenomes, than from SEED-classified shotgun metagenome reads. Finally, based on prior knowledge of the biocrust communities, the SSU-based datasets more accurately identified the dominant biocrust cyanobacteria sequences compared to the shotgun metagenome datasets.

Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long‐term elevated CO2

Biological soil crusts (biocrusts) cover soil surfaces in many drylands globally. The impacts of 10 years of elevated atmospheric CO2 on the cyanobacteria in biocrusts of an arid shrubland were examined at a large manipulated experiment in Nevada, USA. Cyanobacteria-specific quantitative PCR surveys of cyanobacteria small-subunit (SSU) rRNA genes suggested a reduction in biocrust cyanobacterial biomass in the elevated CO2 treatment relative to the ambient controls. Additionally, SSU rRNA gene libraries and shotgun metagenomes showed reduced representation of cyanobacteria in the total microbial community. Taxonomic composition of the cyanobacteria was similar under ambient and elevated CO2 conditions, indicating the decline was manifest across multiple cyanobacterial lineages. Recruitment of cyanobacteria sequences from replicate shotgun metagenomes to cyanobacterial genomes representing major biocrust orders also suggested decreased abundance of cyanobacteria sequences across the majority of genomes tested. Functional assignment of cyanobacteria-related shotgun metagenome sequences indicated that four subsystem categories, three related to oxidative stress, were differentially abundant in relation to the elevated CO2 treatment. Taken together, these results suggest that elevated CO2 affected a generalized decrease in cyanobacteria in the biocrusts and may have favoured cyanobacteria with altered gene inventories for coping with oxidative stress.

From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways. Additional publication details Publication type Book chapter Publication Subtype Book Chapter Title From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8 DOI 10.7208/chicago/9780226196336.001.0001 Year Published 2015 Language English Publisher Chicago University Press Publisher location Chicago, IL Contributing office(s) Forest and Rangeland Ecosystem Science Center Larger Work Type Book Heres how you know From bacteria t elephant : Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8 Larger Work Subtype Monograph Larger Work Title Serengeti IV: Sustaining biodiversity in a coupled human-natural system Other Geospatial Serengeti-Mara ecosystem DOI Privacy Policy | Legal | Accessibility | Site Map | Contact USGS U.S. Department of the Interior | DOI Inspector General | White House | E-gov | No Fear Act | FOIA Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.... From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8. From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8. DOI. 10.7208/chicago/9780226196336.001.0001.