scholarly journals Stratification in Microbial Communities with Depth and Redox Status in a Eutrophic Lake Across Two Years

2021 ◽  
Author(s):  
Robert A Marick ◽  
Benjamin D. Peterson ◽  
Katherine McMahon
Keyword(s):  
Microbial Communities ◽  
Microbial Community Composition ◽  
Open Water ◽  
Redox Status ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Metabolic Potential ◽  
Lake Ecosystems ◽  
The Impact

Bacteria have a profound impact on many key biogeochemical cycles in freshwater lake ecosystems; in turn, the composition of bacteria in the lake is contingent on the chemistry of the water. Many parameters that affect bacterial growth in freshwater ecosystems, such as water temperature, nutrient levels, and redox status, exhibit notable inter-annual differences in addition to seasonal changes. However, little is known about the impact of these inter- and intra-annual differences on the freshwater microbiome, especially in anoxic bottom waters. In this study, we paired biogeochemical field data with 16S rRNA gene amplicon sequencing of depth-discrete samples from a dimictic lake across two open-water seasons to observe variation in the microbiome relative to differences in water chemistry between two years. We found differences in the timing anoxia onset and the redox status in the water column across the two years. Changes in redox status led to major shifts in the microbial community composition. While there was little variation between years in the microbial taxonomic composition at the phyla level, there was substantial interannual variation at more resolved taxonomic levels. Some interannual differences can be explained by links between the predicted metabolic potential of those lineages and the different redox conditions between the two years. These results emphasize the need for repeated monitoring to deduce long-term trends in microbial communities in natural ecosystems and the importance of a comprehensive evaluation of environmental conditions contemporary with any microbiome analysis.

scholarly journals Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5648 ◽  
Author(s):  
Jiayu Li ◽  
Jiayi Lin ◽  
Chenyu Pei ◽  
Kaitao Lai ◽  
Thomas C. Jeffries ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Secondary Forest ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Phosphorus Concentration ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Soil Microbial ◽  
Local Soil

Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.

scholarly journals Wine terroir and the soil microbiome: an amplicon sequencing–based assessment of the Barossa Valley and its sub-regions

2020 ◽  
Author(s):  
Jia Zhou ◽  
Timothy R. Cavagnaro ◽  
Roberta De Bei ◽  
Tiffanie M. Nelson ◽  
John R. Stephen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Community Composition ◽  
Geographic Distance ◽  
Hypervariable Region ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Wine Quality ◽  
The Impact

AbstractSoil is an important factor that contributes to the uniqueness of a wine produced by vines grown in specific conditions. Recent data shows that the composition, diversity and function of soil microbial communities may play important roles in determining wine quality and indirectly affect its economic value. Here, we evaluated the impact of environmental variables on the soil microbiomes of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) caused more microbial dissimilarity than geographic distance. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in microbial community composition were significantly associated with differences in fruit traits and in wine chemical and metabolomic profiles, highlighting the potential influence of microbial communities on the phenotype of grapevines. Our results suggest that environmental factors affect wine terroir, and this may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil microbiomes.

scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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.

Selective Bacterial Community Enrichment Between the Pitcher Plants Sarracenia Minor and Sarracenia Flava

2020 ◽  
Author(s):  
Nikolas M. Stasulli ◽  
Scott M. Yourstone ◽  
Ilon Weinstein ◽  
Elizabeth Ademski ◽  
Elizabeth A. Shank
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Prey Availability ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Community Members ◽  
Pitcher Plants ◽  
Naturally Occurring

Abstract BackgroundThe interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cup-like leaf structures of some carnivorous plants, including the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava, when sampled at the same geographic location and time, cultivate unique microbiota; an indication of biotic selection of microbes due to eliminating many of the environmental variable present in other studies comparing samples harvested over several time points. ResultsDNA was extracted from the decomposing detritus trapped in the base of each Sarracenia leaf pitcher. We profiled a portion of the 16S rRNA gene across the bacterial community members present in this detritus using Illumina MiSeq technology. We identified a surprising amount of diversity within each pitcher, but also discovered that the two Sarracenia species each contained distinct, enriched microbial community members. This suggests a non-random establishment of microbial communities within these two Sarracenia species.ConclusionsOverall, our results indicate that microbial selection is occurring within the pitchers of these two closely related plant species, which is not due to factors such as geographic location, weather, or prey availability. This suggests that specific features of S. minor and S. flava may play a role in fostering specific insect-decomposing microbiomes. These naturally occurring microbial ecosystems can be developed to answer important questions about microbial community succession, disruption, and member contributions to the community. This study will help further establish carnivorous pitcher plants as a model system for studying confined, naturally occurring bacterial communities.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

Water management and phenology influence the root-associated rice field microbiota

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Matteo Chialva ◽  
Stefano Ghignone ◽  
Paolo Cozzi ◽  
Barbara Lazzari ◽  
Paola Bonfante ◽  
...  
Keyword(s):  
Water Management ◽  
Microbial Communities ◽  
Rice Field ◽  
Water Status ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Upland Conditions ◽  
The Impact ◽  
Comprehensive Study

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

scholarly journals A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples

2020 ◽  
Author(s):  
Federica Pinto ◽  
Moreno Zolfo ◽  
Francesco Beghini ◽  
Federica Armanini ◽  
Francesco Asnicar ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Genetic Material ◽  
Amplicon Sequencing ◽  
Sample Type ◽  
Natural Ecosystems ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Water And Sediment Samples

AbstractCultivation-free metagenomic analysis afforded unprecedented details on the diversity, structure and potential functions of microbial communities in different environments. When employed to study the viral fraction of the community that is recalcitrant to cultivation, metagenomics can shed light into the diversity of viruses and their role in natural ecosystems. However, despite the increasing interest in virome metagenomics, methodological issues still hinder the proper interpretation and comparison of results across studies. Virome enrichment experimental protocols are key multi-step processes needed for separating and concentrating the viral fraction from the whole microbial community prior to sequencing. However, there is little information on their efficiency and their potential biases. To fill this gap, we used metagenomic and amplicon sequencing to examine the microbial community composition through the serial filtration and concentration steps commonly used to produce viral-enriched metagenomes. The analyses were performed on water and sediment samples from an Alpine lake. We found that, although the diversity of the retained microbial communities declined progressively during the serial filtration, the final viral fraction contained a large proportion (from 10% to 40%) of non-viral taxa, and that the efficacy of filtration showed biases based on taxonomy. Our results quantified the amount of bacterial genetic material in viromes and highlighted the influence of sample type on the enrichment efficacy. Moreover, since viral-enriched samples contained a significant portion of microbial taxa, computational sequence analysis should account for such biases in the downstream interpretation pipeline.ImportanceFiltration is a commonly used method to enrich viral particles in environmental samples. However, there is little information on its efficiency and potential biases on the final result. Using a sequence-based analysis on water and sediment samples, we found that filtration efficacy is dependent on sample type and that the final virome contained a large proportion of non-viral taxa. Our finding stressed the importance of downstream analysis to avoid biased interpretation of data.

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.

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