Archaeal community dynamics in biogas fermentation at various temperatures assessed by mcrA amplicon sequencing using different primer pairs

Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

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The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

Biogeosciences Discussions ◽

10.5194/bgd-12-18103-2015 ◽

2015 ◽

Vol 12 (21) ◽

pp. 18103-18150 ◽

Cited By ~ 3

Author(s):

L. Purkamo ◽

M. Bomberg ◽

R. Kietäväinen ◽

H. Salavirta ◽

M. Nyyssönen ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Fixation ◽

Keystone Species ◽

Carbon Assimilation ◽

Sugar Metabolism ◽

Archaeal Community ◽

Amino Sugar ◽

Amplicon Sequencing ◽

Fracture Zones ◽

Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

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Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa101 ◽

2020 ◽

Vol 96 (7) ◽

Author(s):

Hidehiro Ishizawa ◽

Masashi Kuroda ◽

Daisuke Inoue ◽

Masaaki Morikawa ◽

Michihiko Ike

Keyword(s):

Plant Growth ◽

Bacterial Communities ◽

Production Efficiency ◽

Community Dynamics ◽

Amplicon Sequencing ◽

Plant Colonization ◽

Plant Growth Promoting Bacteria ◽

Short Period ◽

Plant Growth Promoting ◽

Growth Promoting

ABSTRACT Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

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Quantitative insights into effects of intrapartum antibiotics and birth mode on infant gut microbiota in relation to well-being during the first year of life

10.1101/2021.11.01.21265735 ◽

2021 ◽

Author(s):

Katri Korpela ◽

Roosa Jokela ◽

Ching Jian ◽

Evgenia Dikareva ◽

Anne Nikkonen ◽

...

Keyword(s):

Gut Microbiota ◽

Community Dynamics ◽

Gastrointestinal Symptoms ◽

Well Being ◽

Amplicon Sequencing ◽

First Year ◽

Rrna Gene ◽

Absolute Abundance ◽

Abundance Estimates ◽

First Year Of Life

Background and aims Caesarean section (CS)-birth and maternally administered intrapartum antibiotics (IP) affect colonization of the neonate. We compared the effects of CS delivery and IP antibiotics on infant gut microbiota development and wellbeing over the first year. To understand the developing community dynamics, we focused on absolute bacterial abundance estimates over relative abundances. Methods We studied 144 healthy infants born between gestational weeks 37-42 vaginally without antibiotics (N=58), with IP penicillin (N=25) or cephalosporin (N=13), or by CS with IP cephalosporin (N=34) or other antibiotics (N=14). Gut microbiota composition and temporal development was analysed at 5-7 time points during the first year of life using 16S rRNA gene amplicon sequencing, complemented with qPCR to obtain absolute abundance estimates in 92 infants. A mediation analysis was carried out to identify taxa linked to gastrointestinal function and discomfort (crying, defecation frequency and signs of gastrointestinal symptoms) and birth interventions. Results Based on absolute abundance estimates, depletion of Bacteroides spp. was specific to CS birth while decreased bifidobacteria and increased Bacilli were common to CS birth and exposure to IP antibiotics in vaginal delivery. Abundance of numerous taxa differed between the birth modes among cephalosporin-exposed infants. Penicillin had a milder impact on the infant gut microbiota than cephalosporin. The effects of both CS birth and IP antibiotics on infant gut microbiota associated with increased gastrointestinal symptoms during the first months. Conclusion CS birth and maternal IP antibiotics have both specific and overlapping effects on infant gut microbiota development. The resulting microbiota deviations were found to associate with gastrointestinal symptoms in infancy.

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Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies

Pathogens ◽

10.3390/pathogens9060428 ◽

2020 ◽

Vol 9 (6) ◽

pp. 428

Author(s):

Christos Papadopoulos ◽

Panagiotis A. Karas ◽

Sotirios Vasileiadis ◽

Panagiota Ligda ◽

Anastasios Saratsis ◽

...

Keyword(s):

Gut Microbiota ◽

Host Species ◽

Archaeal Community ◽

Amplicon Sequencing ◽

Structural Effect ◽

Rrna Gene ◽

Host Genotype ◽

Operational Taxonomic Units ◽

Phlebotomine Sandflies ◽

Leishmania Spp

Phlebotomine sandflies are vectors of the humans’ and mammals’ parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P. papatasi, P. neglectus, P. tobbi, and P. similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P. papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P. tobbi and P. similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.

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Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

Applied and Environmental Microbiology ◽

10.1128/aem.04054-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2525-2533 ◽

Cited By ~ 43

Author(s):

Daniel J. O'Sullivan ◽

Paul D. Cotter ◽

Orla O'Sullivan ◽

Linda Giblin ◽

Paul L. H. McSweeney ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Community Dynamics ◽

Microbial Population ◽

Amplicon Sequencing ◽

Production Cycle ◽

Microbial Composition ◽

Temporal And Spatial Distribution ◽

Content Type ◽

Temporal And Spatial

ABSTRACTWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the generaThermus,Pseudoalteromonas, andBifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

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Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany

Journal of Paleolimnology ◽

10.1007/s10933-021-00206-9 ◽

2021 ◽

Author(s):

Ebuka C. Nwosu ◽

Achim Brauer ◽

Jérôme Kaiser ◽

Fabian Horn ◽

Dirk Wagner ◽

...

Keyword(s):

Lake Sediments ◽

Community Dynamics ◽

Abiotic Factors ◽

Variation Partitioning ◽

Amplicon Sequencing ◽

Cyanobacterial Community ◽

Ne Germany ◽

Lipid Biomarker ◽

Biomarker Analysis ◽

Lake Circulation

AbstractSince the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, δ13C data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.

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Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

Animal Microbiome ◽

10.1186/s42523-021-00136-x ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Katelyn Mika ◽

Alexander S. Okamoto ◽

Neil H. Shubin ◽

David B. Mark Welch

Keyword(s):

Bacterial Community ◽

Embryonic Development ◽

Community Dynamics ◽

Internal Surface ◽

Amplicon Sequencing ◽

Phylogenetic Position ◽

Published Data ◽

Bacterial Phyla ◽

Bacterial Community Dynamics ◽

Egg Capsule

Abstract Background Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology. Methods To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST. Results We identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Conclusions Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

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Temporal Microbial Community Dynamics within a Unique Acid Saline Lake

10.1101/2020.12.17.423355 ◽

2020 ◽

Author(s):

Noor-ul-Huda Ghori ◽

Michael. J. Wise ◽

Andrew. S. Whiteley

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Microbial Interactions ◽

Sediment Layer ◽

Microbial Community Dynamics ◽

One Year ◽

Survival Mechanisms ◽

Very High

AbstractLake Magic is one of the acidic hypersaline lakes (ca. 1 km in diameter) present within the Yilgarn Craton in WA. This unique lake exhibits extremely low pH (<1.6) coupled to very high salinity (32% TDS) with the highest concentration of aluminium (1774 mg/L) and silica (510 mg/L) in the world. Previous studies on Lake Magic diversity has revealed that the lake hosts acidophilic, acidotolerant, halophilic and halotolerant bacterial species. These studies provide indicators of the population residing within the lake. However, they do not emphasize the survival mechanisms adopted by the resident microorganisms and how the diversity of microbial populations residing within the lake changes during the dynamic stages of flooding, evapo-concentration and desiccation. We have studied the bacterial and fungal diversity in Lake Magic via amplicon sequencing and functional analysis through different stages of the lake in a span of one year, in the salt and sediment layer. Our results highlight that the diversity in Lake Magic is strongly driven by the pH and salt concentrations at different stages of the lake. The microbial community becomes more specialised in specific functions during more extreme stages. This also suggests that microbial interactions are involved in stabilising the ecosystem and is responsible for the resistance and resilience of these communities as the interactions of these microbes create a safe haven for other microbes to survive during more extreme stages.

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Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Journal of Fungi ◽

10.3390/jof7090686 ◽

2021 ◽

Vol 7 (9) ◽

pp. 686

Author(s):

María Julia Carbone ◽

Sandra Alaniz ◽

Pedro Mondino ◽

Matías Gelabert ◽

Ales Eichmeier ◽

...

Keyword(s):

Drought Stress ◽

Microbial Communities ◽

Community Dynamics ◽

Mycorrhizal Fungus ◽

Arbuscular Mycorrhizal ◽

Field Capacity ◽

Amplicon Sequencing ◽

Bulk Soil ◽

Foot Disease ◽

The Impact

Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO4 when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

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