scholarly journals Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

2008 ◽  
Vol 74 (5) ◽  
pp. 1620-1633 ◽  
Author(s):  
Colleen M. Hansel ◽  
Scott Fendorf ◽  
Phillip M. Jardine ◽  
Christopher A. Francis
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
Spatial Heterogeneity ◽  
Microbial Communities ◽  
Soil Profile ◽  
Soil Depth ◽  
Soil Aggregates ◽  
Archaeal Community ◽  
Biological Properties ◽  
Metabolic Potential

ABSTRACT Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

scholarly journals Metagenome assembled genomes of novel taxa from an acid mine drainage environment

2021 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
Acid Mine

Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

scholarly journals Microbial subnetworks related to short-term diel O2fluxes within geochemically distinct freshwater wetlands

2018 ◽  
Author(s):  
Dean J. Horton ◽  
Matthew J. Cooper ◽  
Anthony J. Wing ◽  
Peter S. Kourtev ◽  
Donald G. Uzarski ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Archaeal Community ◽  
Freshwater Wetlands ◽  
Freshwater Wetland ◽  
Short Term ◽  
Wetland Ecosystems ◽  
Biogeochemical Transformations ◽  
Physical And Chemical

ABSTRACTO2concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis, and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel dramatic physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. However, when exploring at finer resolutions of the microbial communities within each wetland, subcommunities within two wetlands were found to correspond to fluctuating O2levels. Microbial taxa that were found to be susceptible to fluctuating O2levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2fluxes, however, specialist taxa may be sensitive to these same fluxes.

scholarly journals Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

2021 ◽  
Vol 12 ◽  
Author(s):  
Pauline Bergsten ◽  
Pauline Vannier ◽  
Alexandra María Klonowski ◽  
Stephen Knobloch ◽  
Magnús Tumi Gudmundsson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Drilling Fluid ◽  
Microbial Colonization ◽  
Maximum Temperature ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
16S Rrna Gene Analysis ◽  
Drill Cores

The island of Surtsey was formed in 1963–1967 on the offshore Icelandic volcanic rift zone. It offers a unique opportunity to study the subsurface biosphere in newly formed oceanic crust and an associated hydrothermal-seawater system, whose maximum temperature is currently above 120°C at about 100m below surface. Here, we present new insights into the diversity, distribution, and abundance of microorganisms in the subsurface of the island, 50years after its creation. Samples, including basaltic tuff drill cores and associated fluids acquired at successive depths as well as surface fumes from fumaroles, were collected during expedition 5059 of the International Continental Scientific Drilling Program specifically designed to collect microbiological samples. Results of this microbial survey are investigated with 16S rRNA gene amplicon sequencing and scanning electron microscopy. To distinguish endemic microbial taxa of subsurface rocks from potential contaminants present in the drilling fluid, we use both methodological and computational strategies. Our 16S rRNA gene analysis results expose diverse and distinct microbial communities in the drill cores and the borehole fluid samples, which harbor thermophiles in high abundance. Whereas some taxonomic lineages detected across these habitats remain uncharacterized (e.g., Acetothermiia, Ammonifexales), our results highlight potential residents of the subsurface that could be identified at lower taxonomic rank such as Thermaerobacter, BRH-c8a (Desulfallas-Sporotomaculum), Thioalkalimicrobium, and Sulfurospirillum. Microscopy images reveal possible biotic structures attached to the basaltic substrate. Finally, microbial colonization of the newly formed basaltic crust and the metabolic potential are discussed on the basis of the data.

scholarly journals Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

2019 ◽  
Vol 7 (9) ◽  
pp. 357 ◽  
Author(s):  
Moonsuk Hur ◽  
Soo-Je Park
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Community Structure ◽  
16S Rrna ◽  
Microbial Communities ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Full Length ◽  
Rrna Gene ◽  
Microbial Composition

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

scholarly journals Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Rui Xu ◽  
Xiaoxu Sun ◽  
Hanzhi Lin ◽  
Feng Han ◽  
Enzong Xiao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Contaminated Soil ◽  
Soil Depth ◽  
Mining Area ◽  
Soil Profiles ◽  
Deep Soil ◽  
Metabolic Potential ◽  
Microbial Adaptation ◽  
Genes Encoding ◽  
C Metabolism

ABSTRACT Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

scholarly journals Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental and anthropogenic factors

2020 ◽  
Author(s):  
Dalit Roth Rosenberg ◽  
Markus Haber ◽  
Joshua Goldford ◽  
Maya Lalzar ◽  
Dikla Aharoonovich ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Environmental Conditions ◽  
Heterotrophic Bacteria ◽  
Environmental Parameters ◽  
Metabolic Potential ◽  
Free Living ◽  
Size Fractions ◽  
Marine Microbial Communities

SummaryIn the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (two years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living vs particle-associated), followed by depth and finally season. The free-living (FL) community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent “blooms” of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: depth and phytoplankton correlated with the FL population, whereas PA bacteria were correlated primarily with season. A significant part of the variability in community structure could not, however, be explained by the measured environmental parameters. The metabolic potential of the PA community, predicted from 16S amplicon data, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.Originality – Significance StatementMarine microbial populations are complex and dynamic, and the environmental drivers of the structure and function of these communities are mostly unclear. Specifically, marine microbial communities change over time, over depth and between particle-associated and free-living size fractions, yet the relative importance of each of these axes of variability is unclear. Our results highlight fundamentally different population dynamics between free-living and particle-associated marine bacteria: free living populations were more similar between seasons, whereas particle-associated populations were highly variable and exhibited “blooms” of specific clades of heterotrophic bacteria. We also suggest that the environmental conditions often measured as part of oceanographic cruises are not enough to explain most of the variability in microbial population structure. We speculate that organismal interactions and the presence of anthropogenic pollution may be also be important yet under-sampled drivers of oligotrophic marine microbial communities.

scholarly journals Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

2020 ◽  
Vol 8 (2) ◽  
pp. 198
Author(s):  
Mingyue Li ◽  
Tiezhu Mi ◽  
Zhigang Yu ◽  
Manman Ma ◽  
Yu Zhen
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Liaohe River ◽  
Estuarine Wetland ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

scholarly journals Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

2020 ◽  
Author(s):  
Márton Szoboszlay ◽  
Christoph C. Tebbe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Spatial Information ◽  
Soil Aggregates ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Ammonium Oxidation ◽  
Soil Microbial ◽  
The Impact

AbstractSequencing PCR-amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates; and thus, ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here we show with a nitrogen-depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg in order to access spatial information on the prokaryotic community structure as indicated by 16S rRNA-gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic communities. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co-occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6 probably representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

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