Microbial communities of upland peat swamps were no different 1 year after a hazard reduction burn

2020 ◽  
Vol 29 (11) ◽  
pp. 1021
Author(s):  
Nicole A. Christiansen ◽  
Kirstie A. Fryirs ◽  
Timothy J. Green ◽  
Grant C. Hose
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
Management Practice ◽  
Organic Content ◽  
Wetland Ecosystems ◽  
Hazard Reduction ◽  
Eastern Australia ◽  
Community Fingerprint ◽  
The Impact

Fire in wetlands is poorly understood, yet hazard reduction burns are a common management practice and bushfires are becoming increasingly prevalent because of climate change. Fire may have long-lasting implications for the microbial component of these wetland ecosystems that regulate carbon and nutrient cycling. The extremely fire-prone Blue Mountains World Heritage Area in south-eastern Australia contains hundreds of endangered peat-forming upland swamps that regularly experience both bushfires and hazard reduction burns. In a before–after control–­impact study, we surveyed the sediment microbial community of these swamps to test the impact of a low-intensity hazard reduction burn. Along with sediment pH, moisture and organic content, we measured gene abundances including those relating to carbon cycling (quantitative PCR (qPCR) of pmoA, mcrA, bacterial 16S rRNA and archaeal 16S rRNA), and bacteria community fingerprint (terminal restriction fragment length polymorphism (T-RFLP)). One year after the hazard reduction burn, there were no significant differences in the gene abundances or microbial community fingerprint that could be attributed to the fire, suggesting that the hazard reduction burn did not have a long-term impact on these microbial communities.

scholarly journals Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough

2010 ◽  
Vol 76 (9) ◽  
pp. 2968-2979 ◽  
Author(s):  
Shingo Kato ◽  
Yoshinori Takano ◽  
Takeshi Kakegawa ◽  
Hironori Oba ◽  
Kazuhiko Inoue ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Organic Content ◽  
Hyperthermophilic Archaea ◽  
Spreading Center ◽  
Rrna Gene ◽  
Hydrothermal Fields

ABSTRACT The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments.

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.

scholarly journals Comparison of Microbial Community Compositions of Two Subglacial Environments Reveals a Possible Role for Microbes in Chemical Weathering Processes

2005 ◽  
Vol 71 (11) ◽  
pp. 6986-6997 ◽  
Author(s):  
Mark Skidmore ◽  
Suzanne P. Anderson ◽  
Martin Sharp ◽  
Julia Foght ◽  
Brian D. Lanoil
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
Blot Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Solute Flux ◽  
Carbonate Dissolution ◽  
Dot Blot ◽  
Dot Blot Hybridization

ABSTRACT Viable microbes have been detected beneath several geographically distant glaciers underlain by different lithologies, but comparisons of their microbial communities have not previously been made. This study compared the microbial community compositions of samples from two glaciers overlying differing bedrock. Bulk meltwater chemistry indicates that sulfide oxidation and carbonate dissolution account for 90% of the solute flux from Bench Glacier, Alaska, whereas gypsum/anhydrite and carbonate dissolution accounts for the majority of the flux from John Evans Glacier, Ellesmere Island, Nunavut, Canada. The microbial communities were examined using two techniques: clone libraries and dot blot hybridization of 16S rRNA genes. Two hundred twenty-seven clones containing amplified 16S rRNA genes were prepared from subglacial samples, and the gene sequences were analyzed phylogenetically. Although some phylogenetic groups, including the Betaproteobacteria, were abundant in clone libraries from both glaciers, other well-represented groups were found at only one glacier. Group-specific oligonucleotide probes were developed for two phylogenetic clusters that were of particular interest because of their abundance or inferred biochemical capabilities. These probes were used in quantitative dot blot hybridization assays with a range of samples from the two glaciers. In addition to shared phyla at both glaciers, each glacier also harbored a subglacial microbial population that correlated with the observed aqueous geochemistry. These results are consistent with the hypothesis that microbial activity is an important contributor to the solute flux from glaciers.

scholarly journals Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liebana ◽  
Soroush Saheb-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Null Models ◽  
Marker Genes ◽  
Experimental Systems ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

scholarly journals Assessment of the petroleum hydrocarbon biodegradation potential of the sediment microbial community from an urban fringing tidal marsh of Northern New England

2018 ◽  
Author(s):  
Sinéad M. Ní Chadhain ◽  
Jarett L. Miller ◽  
John P. Dustin ◽  
Jeff P. Trethewey ◽  
Stephen H. Jones ◽  
...  
Keyword(s):  
16S Rrna ◽  
New England ◽  
Microbial Communities ◽  
Tidal Marsh ◽  
Tidal Marshes ◽  
Hydrocarbon Biodegradation ◽  
Alkane Hydroxylase ◽  
Great Bay Estuary ◽  
Functional And Phylogenetic Diversity ◽  
The Impact

AbstractWe assessed the impact of dodecane,n-hexane and gasoline on the microbial diversity of chronically polluted fringing tidal marsh sediment from the Great Bay Estuary of New Hampshire. Dilution cultures containing saturated alkane concentrations were sampled at zero, one and 10 days, andalkBandcyp153A1alkane hydroxylase gene libraries and 16S rRNA sequences were analyzed. The initial sediment had the most diverse alkane hydroxylase sequences and phylogenetic composition whereas treated sediments became less functionally and phylogenetically diverse with alkane substrates apparently enriching a few dominant taxa. All 1-and 10-day samples were dominated byPseudomonas-type alkane hydroxylase sequences except in dodecane treatments where primarilyRhodococcus--type alkane hydroxylases were detected. 16S rRNA profiling revealed that the Gammaproteobacteria, particularlyPseudomonas, dominated all one day samples, especially then-hexane and gasoline treatments (63.2 and 47.2% respectively) and the 10-dayn-hexane treatment (which contained 60.8%Pseudomonasand 18.6%Marinobacter).In contrast, the 10 days of dodecane treatment enriched for Actinobacteria (26.2%Rhodococcusand 32.4%Mycobacterium)and gasoline treatment enriched for Firmicutes (29.7%; mainlyBacillus, LysinibacillusandRumelibacillus).Our data indicate that fringing tidal marshes contain microbial communities with alkane-degrading abilities similar to larger meadow marshes, and support the hypothesis that alkane exposure reduces the functional and phylogenetic diversity of microbial communities in an alkane-specific manner. Further research to evaluate the ability of such fringing marsh communities to rebound to pre-pollutant diversity levels should be conducted to better assess the threat of petroleum to these habitats.

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 Different Active Microbial Communities in Two Contrasted Subantarctic Fjords

2021 ◽  
Vol 12 ◽  
Author(s):  
Claudia Maturana-Martínez ◽  
Camila Fernández ◽  
Humberto E. González ◽  
Pierre E. Galand
Keyword(s):  
Climate Change ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
Standing Stock ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biogeochemical Processes ◽  
Biogeographic Patterns ◽  
Group I

Microorganisms play a crucial role in biogeochemical processes affecting the primary production and biogeochemical cycles of the ocean. In subpolar areas, the increment of the water temperature induced by climate change could lead to changes in the structure and activity of planktonic microbial communities. To understand how the structure of the microbial community in Chilean Patagonian fjords could be affected by climate change, we analyzed the composition of the prokaryotic community (bacteria-archaea) in two fjords (Pia and Yendegaia) with contrasting morphological and hydrological features. We targeted both the standing stock (16S rRNA genes) and the active fraction (16S rRNA transcripts) of the microbial communities during two consecutive austral winters. Our results showed that in both fjords, the active community had higher diversity and stronger biogeographic patterns when compared to the standing stock. Members of the Alpha-, Gamma-, and Deltaproteobacteria followed by archaea from the Marine Group I (Thaumarchaeota) dominated the active communities in both fjords. However, in Pia fjord, which has a marine-terminating glacier, the composition of the microbial community was directly influenced by the freshwater discharges from the adjacent glacier, and indirectly by a possible upwelling phenomenon that could bring deep sea bacteria such as SAR202 to the surface layer. In turn, in the Yendegaia, which has a land-terminating glacier, microbial communities were more similar to the ones described in oceanic waters. Furthermore, in Yendegaia fjord, inter-annual differences in the taxonomic composition and diversity of the microbial community were observed. In conclusion, Yendegaia fjord, without glacier calving, represents a fjord type that will likely be more common under future climate scenarios. Our results showing distinct Yendegaia communities, with for example more potential nitrogen-fixing microorganisms (Planctomycetes), indicate that as a result of climate change, changing planktonic communities could potentially impact biogeochemical processes and nutrient sources in subantarctic fjords.

scholarly journals A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7332
Author(s):  
Miguel David Marfil-Santana ◽  
Anahí Martínez-Cárdenas ◽  
Analuisa Ruíz-Hernández ◽  
Mario Vidal-Torres ◽  
Norma Angélica Márquez-Velázquez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Secondary Metabolite ◽  
Resistant Bacteria ◽  
Mangrove Sediments ◽  
Molecular Networking ◽  
Mangrove Tree ◽  
Enhanced Production ◽  
The Impact

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

scholarly journals Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues

2020 ◽  
Author(s):  
Anna Christine Trego ◽  
Sarah O'Sullivan ◽  
Simon Mills ◽  
Estefania Porca ◽  
Christopher Quince ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Size Fraction ◽  
Methanogenic Archaea ◽  
Organic Content ◽  
Environmental Cues ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Methanogenic Activity ◽  
Fermentative Bacteria

Abstract Background In this study, individual anaerobic granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates originated from three different biomass sources, i.e. three different engineered biological wastewater treatment systems, were each size-separated into three fractions – small, medium and large – and characterised according to organic matter concentrations and rates of methanogenic activity. Differences in the microbial community structure of each size fraction from each source were determined using 16S rRNA gene sequencing. Subsequently, single granules from the large size fraction of one of the sources were separately subjected controlled environmental cues in novel micro batch reactors (mBRs). Results Organic content, methanogenic activity, and microbial community were significantly different between the three size fractions, with diversity trajectories replicated across the three sludge sources – indicating a potential development model as granules age. Individual large granules from one of these sources were statistically identical with respect to the structure of the active community based on cDNA analysis. It was observed that the active microbial community of individual granules, at the depth of 16S rRNA sequencing, produced reproducible responses to environmental conditions. While each condition resulted in the up-regulation of particular OTUs and clades, the core microbiome, consisting of many fermentative bacteria along with methanogenic archaea, namely, Methanosarcina and Methanobacterium , persisted. Conclusions At this level, single anaerobic granules can be considered highly-replicated whole-ecosystems, opening the door to high-throughput studies in Microbial Ecology.

scholarly journals 16S rRNA Gene Amplicon Sequencing of Microbial Communities Involved in Anaerobic Bulking in a Mesophilic Expanded Granular Sludge Bed Reactor Treating Wastewater Discharged from a Japanese-Style Thickened Worcestershire Sauce-Producing Factory

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Takeshi Yamada ◽  
Jun Harada ◽  
Yuki Okazaki ◽  
Tsuyoshi Yamaguchi ◽  
Atsushi Nakano
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Granular Sludge ◽  
Amplicon Sequencing ◽  
Organic Content ◽  
Rrna Gene ◽  
Sludge Bulking ◽  
High Organic Content

We analyzed the prokaryotes in bulking and healthy sludge from a mesophilic expanded granular sludge bed reactor treating wastewater with high organic content by 16S rRNA gene amplicon sequencing. We tabulated the microbiota at the phylum level, providing a framework for avoiding sludge bulking.

Sign in / Sign up

Export Citation Format

Share Document