scholarly journals Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

2020 ◽  
Author(s):  
Kathrin Busch ◽  
Lindsay Beazley ◽  
Ellen Kenchington ◽  
Frederick Whoriskey ◽  
Beate Slaby ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Anthropogenic Activities ◽  
Amplicon Sequencing ◽  
Habitat Destruction ◽  
Artificial Substrates ◽  
Rrna Gene ◽  
Anthropogenic Pressures ◽  
Glass Sponge

ABSTRACTEstablishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from pristine sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in sponges and environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

scholarly journals Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

2020 ◽  
Vol 21 (6) ◽  
pp. 1001-1010 ◽  
Author(s):  
Kathrin Busch ◽  
Lindsay Beazley ◽  
Ellen Kenchington ◽  
Frederick Whoriskey ◽  
Beate M. Slaby ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Anthropogenic Activities ◽  
Amplicon Sequencing ◽  
Habitat Destruction ◽  
Artificial Substrates ◽  
Rrna Gene ◽  
Anthropogenic Pressures ◽  
Glass Sponge

Abstract Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from protected sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in the four sponges from this site and the environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

scholarly journals Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

2021 ◽  
Vol 8 ◽  
Author(s):  
Elisa Banchi ◽  
Paola Del Negro ◽  
Mauro Celussi ◽  
Francesca Malfatti
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Marine Ecosystem ◽  
Amplicon Sequencing ◽  
Cell Interaction ◽  
Venice Lagoon ◽  
Minor Role ◽  
Rrna Gene ◽  
A Minor ◽  
Cell Cell

Sediment microbial communities play essential roles in marine ecosystem functioning. Their study is crucial to understand how environmental conditions affect microbial diversity and biogeochemical cycles. The Venice Lagoon, one of the largest Adriatic transitional systems, is subjected to different natural and anthropogenic stressors. In this study, surface sediments microbial communities were finely characterized using 16S rRNA gene amplicon sequencing and metagenomics. Samples were collected seasonally in 2019 and 2020 at different sites within Lagoon sub-basins. Our results indicated a stable spatial distribution of the sediment microbiome: salinity, grain size, and total organic carbon were found to be important drivers in shaping prokaryotic communities, while temperature had a minor role. We detected high microbial diversity at all stations, mainly due to low abundant taxa: bacteria represented the vast majority of the reads (∼96.1%), with Woeseia the most abundant genus (∼4.4%). The metagenomic analysis highlighted significant differences among sites in terms of biogeochemical processes (e.g., C, N, Fe, and S metabolism), and cell-cell interaction strategies (e.g., mobilome, regulations and cell signaling). Chioggia, a sandy site subjected to marine influence, presented the highest abundance of ammonia-oxidizing archaeon Candidatus Nitrosopumilus, in accordance with the highest amount of ammonia monooxygenase subunit genes. At the same site, sulfate-reducing bacteria (Desulfobacteria and Desulfobacterales) and sulfur-related genes were found in lower abundance. Marghera and Tresse, the most polluted sites, showed higher abundance of sewage-related bacteria and antibiotic and toxic compound resistance genes. Furthermore, these sites showed higher amount of genes related to cell-cell interaction, such as pathogenicity islands, transposable-elements, and biofilm formation. Our findings highlighted that sediment features and human-related activities have profound and long-term impacts on the surface sediment microbial communities of the Venice Lagoon.

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 A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Davide Porcellato ◽  
Roger Meisal ◽  
Alberto Bombelli ◽  
Judith A. Narvhus
Keyword(s):  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Lactation Period ◽  
Strong Negative Correlation ◽  
Udder Health ◽  
Milk Samples ◽  
Lactating Cows ◽  
Definition Of ◽  
The 16S Rrna Gene

AbstractThe importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing

2020 ◽  
Vol 178 ◽  
pp. 115815 ◽  
Author(s):  
Theo Y.C. Lam ◽  
Ran Mei ◽  
Zhuoying Wu ◽  
Patrick K.H. Lee ◽  
Wen-Tso Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Full Length ◽  
Rrna Gene ◽  
Anaerobic Digesters

scholarly journals Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore

2021 ◽  
Author(s):  
Lindsey K. Deignan ◽  
Diane McDougald
Keyword(s):  
Climate Change ◽  
16S Rrna ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Amplicon Sequencing ◽  
Post Transplantation ◽  
Reciprocal Transplantation ◽  
Adaptive Resilience ◽  
Stressful Environments ◽  
Conservation And Management

AbstractAs corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome’s response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.

scholarly journals Cellulolytic and Xylanolytic Microbial Communities Associated With Lignocellulose-Rich Wheat Straw Degradation in Anaerobic Digestion

2021 ◽  
Vol 12 ◽  
Author(s):  
Mads Borgbjerg Jensen ◽  
Nadieh de Jonge ◽  
Maja Duus Dolriis ◽  
Caroline Kragelund ◽  
Christian Holst Fischer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Wheat Straw ◽  
Lignocellulosic Biomass ◽  
Correlation Method ◽  
Amplicon Sequencing ◽  
Lignocellulose Degradation ◽  
Rrna Gene ◽  
Key Species

The enzymatic hydrolysis of lignocellulosic polymers is generally considered the rate-limiting step to methane production in anaerobic digestion of lignocellulosic biomass. The present study aimed to investigate how the hydrolytic microbial communities of three different types of anaerobic digesters adapted to lignocellulose-rich wheat straw in continuous stirred tank reactors operated for 134 days. Cellulase and xylanase activities were monitored weekly using fluorescently-labeled model substrates and the enzymatic profiles were correlated with changes in microbial community compositions based on 16S rRNA gene amplicon sequencing to identify key species involved in lignocellulose degradation. The enzymatic activity profiles and microbial community changes revealed reactor-specific adaption of phylogenetically different hydrolytic communities. The enzymatic activities correlated significantly with changes in specific taxonomic groups, including representatives of Ruminiclostridium, Caldicoprobacter, Ruminofilibacter, Ruminococcaceae, Treponema, and Clostridia order MBA03, all of which have been linked to cellulolytic and xylanolytic activity in the literature. By identifying microorganisms with similar development as the cellulase and xylanase activities, the proposed correlation method constitutes a promising approach for deciphering essential cellulolytic and xylanolytic microbial groups for anaerobic digestion of lignocellulosic biomass.

scholarly journals Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

2019 ◽  
Author(s):  
Wenjing Qiao ◽  
Luz A. Puentes Jácome ◽  
Xianjin Tang ◽  
Line Lomheim ◽  
Minqing Ivy Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Molar Ratio ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
Hch Isomers ◽  
Persistent Pesticide ◽  
Hexachlorocyclohexane Isomers ◽  
Archaeal Communities

AbstractIntensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient γ-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3 µM/day to ∼12 µM/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from β (0.77±0.15), α (0.55±0.09), γ (0.13±0.02) to δ (0.06±0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance of Pelobacter and Dehalobacter, especially in the α-HCH and δ-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

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

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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