Simultaneous organics, sulphate and salt removal in a microbial desalination cell with an insight into microbial communities

Abstract Abstract Background Since animals frequently encounter a variety of harmful fungi in nature, their ability to develop sophisticated anti-fungal strategies allows them to flourish across the globe. Extensive studies have highlighted the significant involvement of indigenous microbial communities in human health. However, the daunting diversity of mammalian microbiota and host genetic complexity are major obstacles to our understanding of these intricate links between microbiota components, host immune genotype, and disease phenotype. In this study, we sought to develop a bacterium-fungus-Drosophilamodel to systematically evaluate the anti-fungal effects of commensal bacteria. Results We isolated the pathogenic fungal strain, Diaporthe FY, which was detrimental to the survival and development of Drosophila upon infection. Using Drosophilaas a model system, Drosophila-associated Lactobacillus plantarumfunctioned as a probiotic, and protected the flies from mortality induced by Diaporthe FY. Our results show that L. plantarumhindered the growth of Diaporthe FYin vitro, and decreased the mortality rate of Diaporthe FY-infected flies in vivo, consequently mitigating the toxicity of Diaporthe FYto the hosts. Additionally, the presence of L. plantarumoverrode the avoidance of oviposition on Diaporthe FY-associated substrates. Conclusions Diaporthe FYwas identified as a potential Drosophilapathogen. Commensal L. plantarummitigated the susceptibility of Drosophilato pathogenic fungi, providing insight into the natural interplay between commensal and pathogenic microbial communities that contribute to animal health and pathogenesis.

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Late Ediacaran organic microfossils from Finland

Geological Magazine ◽

10.1017/s0016756821000753 ◽

2021 ◽

pp. 1-14

Author(s):

Sebastian Willman ◽

Ben J. Slater

Keyword(s):

Microbial Communities ◽

Microbial Mats ◽

Trace Fossils ◽

Impact Structure ◽

Meteorite Impact ◽

Fine Grained ◽

Body Fossil ◽

New Evidence ◽

Insight Into ◽

Direct Body

Abstract Here we present a detailed accounting of organic microfossils from late Ediacaran sediments of Finland, from the island of Hailuoto (northwest Finnish coast), and the Saarijärvi meteorite impact structure (~170 km northeast of Hailuoto, mainland Finland). Fossils were recovered from fine-grained thermally immature mudstones and siltstones and are preserved in exquisite detail. The majority of recovered forms are sourced from filamentous prokaryotic and protistan-grade organisms forming interwoven microbial mats. Flattened Nostoc-ball-like masses of bundled Siphonophycus filaments are abundant, alongside Rugosoopsis and Palaeolyngbya of probable cyanobacterial origin. Acritarchs include Chuaria, Leiosphaeridia, Symplassosphaeridium and Synsphaeridium. Significantly, rare spine-shaped sclerites of bilaterian origin were recovered, providing new evidence for a nascent bilaterian fauna in the terminal Ediacaran. These findings offer a direct body-fossil insight into Ediacaran mat-forming microbial communities, and demonstrate that alongside trace fossils, detection of a bilaterian fauna prior to the Cambrian might also be sought among the emerging record of small carbonaceous fossils (SCFs).

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The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities

mSystems ◽

10.1128/msystems.00587-19 ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Thomas Yssing Michaelsen ◽

Jakob Brandt ◽

Caitlin Margaret Singleton ◽

Rasmus Hansen Kirkegaard ◽

Johanna Wiesinger ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Antisense Rna ◽

Antisense Transcription ◽

Individual Species ◽

Data Sets ◽

Antisense Expression ◽

Noise Characteristics ◽

Starting Point ◽

Insight Into

ABSTRACT High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities. IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

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Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

Microorganisms ◽

10.3390/microorganisms8101614 ◽

2020 ◽

Vol 8 (10) ◽

pp. 1614

Author(s):

Yue Zheng ◽

Huan Wang ◽

Zheng Yu ◽

Fauzi Haroon ◽

Maria E. Hernández ◽

...

Keyword(s):

Microbial Communities ◽

Nitrosative Stress ◽

Community Members ◽

Functional Guilds ◽

Stress Response Genes ◽

Hypoxic Conditions ◽

Partial Pressures ◽

Carbon Transfer ◽

Multiple Samples ◽

Insight Into

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.

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Insight into the microbial communities associated with first larval stages of Mytilus galloprovincialis: Possible interference by estrogenic compounds

Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology ◽

10.1016/j.cbpc.2020.108833 ◽

2020 ◽

Vol 237 ◽

pp. 108833

Author(s):

T. Balbi ◽

L. Vezzulli ◽

A. Lasa ◽

A. Pallavicini ◽

L. Canesi

Keyword(s):

Microbial Communities ◽

Mytilus Galloprovincialis ◽

Estrogenic Compounds ◽

Larval Stages ◽

Insight Into

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The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats

mBio ◽

10.1128/mbio.00560-16 ◽

2016 ◽

Vol 7 (4) ◽

Cited By ~ 78

Author(s):

Alejandra Hernandez-Agreda ◽

William Leggat ◽

Pim Bongaerts ◽

Tracy D. Ainsworth

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Microbial Interactions ◽

Environmental Distribution ◽

Core Microbiome ◽

Spatial And Temporal Scales ◽

Select Group ◽

Mechanistic Basis ◽

Number Of Bacteria ◽

Insight Into

ABSTRACT For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts’ environment. IMPORTANCE Corals have been proposed as the most diverse microbial biosphere. The high variability of microbial communities has hampered the identification of bacteria playing key functional roles that contribute to coral survival. Exploring the bacterial community in a coral with a broad environmental distribution, we found a group of bacteria present across all environments and a higher number of bacteria consistently associated with mesophotic corals (60 to 80 m). These results provide evidence of consistent and ubiquitous coral-bacterial partnerships and support the consideration of corals as metaorganisms hosting three functionally distinct microbiomes: a ubiquitous core microbiome, a microbiome filling functional niches, and a highly variable bacterial community.

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Microbial communities in northern Adriatic mucilaginous aggregates: insight into the early phase of aggregate formation

Hydrobiologia ◽

10.1007/s10750-010-0474-6 ◽

2010 ◽

Vol 658 (1) ◽

pp. 213-220 ◽

Cited By ~ 3

Author(s):

Maria Blažina ◽

Mirjana Najdek ◽

Dragica Fuks ◽

Nenad Smodlaka

Keyword(s):

Microbial Communities ◽

Early Phase ◽

Aggregate Formation ◽

Northern Adriatic ◽

Insight Into

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First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry

Microorganisms ◽

10.3390/microorganisms9071521 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1521

Author(s):

Margarita Shevchenko ◽

Stanislav Sukhikh ◽

Olga Babich ◽

Svetlana Noskova ◽

Svetlana Ivanova ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Biofilms ◽

Cellulolytic Activity ◽

Antimicrobial Compounds ◽

Natural Habitats ◽

The Matrix ◽

Kaliningrad Region ◽

Dominant Bacteria ◽

Insight Into ◽

Antibacterial Potential

Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial communities of the flooded Walter amber quarry (Kaliningrad region, Russia). As a result of 16S rDNA high-throughput profiling, 127 genera of bacteria belonging to 12 phyla of bacteria were found in sediment samples: Acidobacteria sp., Actinobacteria sp., Armatimonadetes sp., Bacteroidetes sp., Chloroflexi sp., Cyanobacteria sp., Firmicutes sp., Gemmatimonadetes sp., Planctomycetes sp., Proteobacteria sp., Tenericutes sp., and Verrucomicrobia sp. The dominant bacteria groups were the families Ruminococcaceae and Lachnospiraceae, belonging to the order Clostridiales phylum Firmicutes. Analysis of enrichment cultures obtained from sediments showed the presence of antibacterial and cellulolytic activity. It seems likely that the bacteria of the studied communities are producers of antimicrobial compounds and have the potential for biotechnological use.

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Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities

10.1101/2020.11.11.378315 ◽

2020 ◽

Author(s):

Caroline S. Fortunato ◽

David A. Butterfield ◽

Benjamin Larson ◽

Noah Lawrence-Slavas ◽

Christopher K. Algar ◽

...

Keyword(s):

Thermal Stress ◽

Microbial Communities ◽

Deep Sea ◽

Nitrate Reduction ◽

Stress Proteins ◽

Lag Time ◽

Stable Isotope Probing ◽

Axial Seamount ◽

Insight Into

AbstractDepressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed an ROV-powered incubator instrument to carry out and compare results from in situ and shipboard RNA Stable Isotope Probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labelled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations suggesting that hydrostatic pressure ameliorated thermal stress in the metabolically active microbes in the seafloor incubations. Together, results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under near-native conditions in the ocean.

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Lineage-Specific Responses of Microbial Communities to Environmental Change

Applied and Environmental Microbiology ◽

10.1128/aem.02226-12 ◽

2012 ◽

Vol 79 (1) ◽

pp. 39-47 ◽

Cited By ~ 17

Author(s):

Nicholas D. Youngblut ◽

Ashley Shade ◽

Jordan S. Read ◽

Katherine D. McMahon ◽

Rachel J. Whitaker

Keyword(s):

Environmental Change ◽

Microbial Communities ◽

Temporal Distribution ◽

Taxonomic Resolution ◽

Ecological Change ◽

Valuable Insight ◽

Content Type ◽

Ecological Patterns ◽

Definition Of ◽

Insight Into

ABSTRACT A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN , to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter . At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

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