Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

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.

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Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

10.1101/197855 ◽

2017 ◽

Author(s):

Eric R Hester ◽

Sarah F. Harpenslager ◽

Josepha MH van Diggelen ◽

Leon L Lamers ◽

Mike SM Jetten ◽

...

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Amplicon Sequencing ◽

N Fertilization ◽

Wetland Soil ◽

N Availability ◽

Gas Emissions ◽

16S Rrna Amplicon Sequencing ◽

N Input

AbstractWetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere ofJuncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations withJ. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

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Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Foods ◽

10.3390/foods9091247 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1247

Author(s):

Emiel Van Reckem ◽

Christina Charmpi ◽

David Van der Veken ◽

Wim Borremans ◽

Luc De Vuyst ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Bacterial Communities ◽

Geographical Origin ◽

Salt Content ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Future Application ◽

Processing Conditions ◽

The Impact

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

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Microgeographic Epidemiology of Malaria Parasites in an Irrigated Area of Western Kenya by Deep Amplicon Sequencing

The Journal of Infectious Diseases ◽

10.1093/infdis/jiaa520 ◽

2020 ◽

Author(s):

Elizabeth Hemming-Schroeder ◽

Daibin Zhong ◽

Solomon Kibret ◽

Amanda Chie ◽

Ming-Chieh Lee ◽

...

Keyword(s):

Malaria Transmission ◽

Environmental Changes ◽

Amplicon Sequencing ◽

Transmission Intensity ◽

Transmission Risk ◽

Irrigated Agriculture ◽

Irrigation Scheme ◽

Malaria Parasites ◽

Irrigated Area ◽

The Impact

Abstract To improve food security, investments in irrigated agriculture are anticipated to increase throughout Africa. However, the extent to which environmental changes from water resource development will impact malaria epidemiology remains unclear. This study was designed to compare the sensitivity of molecular markers used in deep amplicon sequencing for evaluating malaria transmission intensities and to assess malaria transmission intensity at various proximities to an irrigation scheme. Compared to ama1, csp, and msp1 amplicons, cpmp required the smallest sample size to detect differences in infection complexity between transmission risk zones. Transmission intensity was highest within 5 km of the irrigation scheme by polymerase chain reaction positivity rate, infection complexity, and linkage disequilibrium. The irrigated area provided a source of parasite infections for the surrounding 2- to 10-km area. This study highlights the suitability of the cpmp amplicon as a measure for transmission intensities and the impact of irrigation on microgeographic epidemiology of malaria parasites.

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

10.21203/rs.3.rs-33130/v1 ◽

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.

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Deciphering the functioning of microbial communities: shedding light on the critical steps in metaproteomics

10.1101/697599 ◽

2019 ◽

Author(s):

Augustin Géron ◽

Johannes Werner ◽

Ruddy Wattiez ◽

Philippe Lebaron ◽

Sabine Matallana-Surget

Keyword(s):

Microbial Communities ◽

Protein Identification ◽

Environmental Changes ◽

Rapid Development ◽

Complex Structure ◽

Molecular Tools ◽

Protein Functions ◽

The Impact ◽

And Oxidative Stress

AbstractUnraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation and provide reliable ecological interpretation, are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting and oxidative stress response were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.

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Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

10.21203/rs.2.19814/v2 ◽

2020 ◽

Author(s):

Kasun H Bodawatta ◽

Katerina Puzejova ◽

Katerina Sam ◽

Michael Poulsen ◽

Knud A. Jønsson

Keyword(s):

Microbial Communities ◽

Digestive Tract ◽

Wild Bird ◽

Anthropogenic Impacts ◽

Parus Major ◽

Amplicon Sequencing ◽

Cloacal Swab ◽

Non Invasive ◽

16S Rrna Amplicon Sequencing ◽

Microbiome Research

Abstract Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

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The impact of bacterial diversity on resistance to biocides in oilfields

Scientific Reports ◽

10.1038/s41598-021-02494-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gabriela Feix Pereira ◽

Harry Luiz Pilz-Junior ◽

Gertrudes Corção

Keyword(s):

Water Samples ◽

Produced Water ◽

Functional Characterization ◽

Amplicon Sequencing ◽

Oil Field ◽

Oil Fields ◽

Sulfate Reducing ◽

16S Rrna Amplicon Sequencing ◽

Dimethyl Benzyl ◽

The Impact

AbstractExtreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and acid-producing bacteria (APB) are usually found in these places and can harm important processes due to increases in corrosion rates, biofouling and reservoir biosouring. Biocides such as glutaraldehyde, dibromo-nitrilopropionamide (DBNPA), tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and alkyl dimethyl benzyl ammonium chloride (ADBAC) are commonly used in oil fields to mitigate uncontrolled microbial growth. The aim of this work was to evaluate the differences among microbiome compositions and their resistance to standard biocides in four different Brazilian produced water samples, two from a Southeast Brazil offshore oil field and two from different Northeast Brazil onshore oil fields. Microbiome evaluations were carried out through 16S rRNA amplicon sequencing. To evaluate the biocidal resistance, the Minimum Inhibitory Concentration (MIC) of the standard biocides were analyzed using enriched consortia of SRB and APB from the produced water samples. The data showed important differences in terms of taxonomy but similar functional characterization, indicating the high diversity of the microbiomes. The APB and SRB consortia demonstrated varying resistance levels against the biocides. These results will help to customize biocidal treatments in oil fields.

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Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

10.1101/680694 ◽

2019 ◽

Author(s):

Sven P. Tobias-Hünefeldt ◽

Stephen R. Wing ◽

Nadjejda Espinel-Velasco ◽

Federico Baltar ◽

Sergio E. Morales

Keyword(s):

Community Structure ◽

New Zealand ◽

Microbial Communities ◽

National Park ◽

Amplicon Sequencing ◽

Forested Catchments ◽

Environmental Forcing ◽

Low Salinity ◽

The Impact ◽

Depth View

SummarySystems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

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Localization of bacterial communities within gut compartments across Cephalotes turtle ants

Applied and Environmental Microbiology ◽

10.1128/aem.02803-20 ◽

2021 ◽

Author(s):

Peter J. Flynn ◽

Catherine L. D’Amelio ◽

Jon G. Sanders ◽

Jacob A. Russell ◽

Corrie S. Moreau

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Digestive Tract ◽

Bacterial Communities ◽

Evolutionary History ◽

Amplicon Sequencing ◽

Caste Differentiation ◽

Animal Group ◽

16S Rrna Amplicon Sequencing ◽

Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

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