scholarly journals Factors that affect the composition and activity of salt marsh microbial communities

2016 ◽  
Author(s):  
Patrick J. Kearns
Keyword(s):  
Salt Marsh ◽  
Microbial Communities

scholarly journals Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

2020 ◽  
Author(s):  
Jeffrey Marlow ◽  
Rachel Spietz ◽  
Keun-Young Kim ◽  
Mark Ellisman ◽  
Peter Girguis ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Marsh Sediment ◽  
Anabolic Activity ◽  
Salt Marsh Sediment ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

scholarly journals Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

2016 ◽  
Vol 82 (9) ◽  
pp. 2862-2871 ◽  
Author(s):  
Christopher J. Graves ◽  
Elizabeth J. Makrides ◽  
Victor T. Schmidt ◽  
Anne E. Giblin ◽  
Zoe G. Cardon ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Nutrient Enrichment ◽  
Nutrient Loading ◽  
Whole Genome ◽  
Sewage Effluent ◽  
Fine Scale ◽  
Functional Responses

ABSTRACTEnvironmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.IMPORTANCEIn this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.

scholarly journals Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments

2000 ◽  
Vol 66 (7) ◽  
pp. 3037-3043 ◽  
Author(s):  
Marc E. Frischer ◽  
Jean M. Danforth ◽  
Michele A. Newton Healy ◽  
F. Michael Saunders
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
Microbial Communities ◽  
Rna Extraction ◽  
Oligonucleotide Probes ◽  
Whole Cell ◽  
Sulfate Reducing ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
Reducing Bacteria

ABSTRACT rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% � 3.7% [mean � standard deviation]) relative to direct DAPI (4′,6′-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r 2 = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond

2017 ◽  
Vol 80 (1) ◽  
pp. 29-41 ◽  
Author(s):  
PJ Kearns ◽  
D Holloway ◽  
JH Angell ◽  
SG Feinman ◽  
JL Bowen
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
Environmental Conditions ◽  
Short Term ◽  
Diel Changes

scholarly journals Effects of ciprofloxacin on salt marsh sediment microbial communities

2007 ◽  
Vol 1 (7) ◽  
pp. 585-595 ◽  
Author(s):  
Ana Lucía Córdova-Kreylos ◽  
Kate M Scow
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
Marsh Sediment ◽  
Salt Marsh Sediment
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