scholarly journals Living Lithic and Sublithic Bacterial Communities in Namibian Drylands

2021 ◽  
Vol 9 (2) ◽  
pp. 235
Author(s):  
Steffi Genderjahn ◽  
Simon Lewin ◽  
Fabian Horn ◽  
Anja M. Schleicher ◽  
Kai Mangelsdorf ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Soil Formation ◽  
Amplicon Sequencing ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Rock Weathering ◽  
Weathering Processes ◽  
Rock Types ◽  
Culture Independent

Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.

scholarly journals Resistance, resilience, and functional redundancy of freshwater microbial communities facing multiple agricultural stressors in a mesocosm experiment

2020 ◽  
Author(s):  
Naíla Barbosa da Costa ◽  
Vincent Fugère ◽  
Marie-Pier Hébert ◽  
Charles C.Y. Xu ◽  
Rowan D.H. Barrett ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Limit Of Detection ◽  
Taxonomic Diversity ◽  
Amplicon Sequencing ◽  
Functional Redundancy ◽  
Rrna Gene ◽  
Freshwater Biodiversity ◽  
Initial State ◽  
Biolog Ecoplates ◽  
Culture Independent

AbstractFreshwater biodiversity is threatened by fertilizers and pesticides from agricultural sources. Microbial communities can be resistant (i.e., community composition stays largely the same) or resilient (i.e., composition changes but then returns to its initial state) to these contaminants. Even after changes in composition, communities may continue to support ecosystem processes due to functional redundancy, in which different taxa carry out the same process, such that the process is maintained even after some taxa are lost. To test the extent of resistance, resilience, and functional redundancy in aquatic bacterial communities (bacterioplankton) faced with agricultural stressors, we exposed freshwater mesocosms to two commonly used pesticides: the herbicide Roundup (glyphosate) and the neonicotinoid insecticide imidacloprid, alone or in combination, and in high or low nutrient backgrounds. Over the 42-day experiment, we tracked bacterial density with flow cytometry, functional composition with Biolog EcoPlates, and taxonomic diversity with culture-independent 16S rRNA gene amplicon sequencing. We show that only glyphosate, but not imidacloprid or nutrients, measurably changed community structure. Despite this change, metabolic capabilities were maintained, suggesting functional redundancy. We further show that communities are resilient at broad, but not fine phylogenetic levels: the precise amplicon sequence variants (ASVs) driven below the limit of detection by glyphosate stress do not return, but tend to be replaced by relatives within the same genus. Together, our results show that bacterioplankton are broadly resistant, resilient, and redundant faced with severe agricultural stressors on weekly time scales, but that high doses of glyphosate can have longer-lasting effects on fine-scale diversity.

scholarly journals Culture-Independent and Culture-Dependent Characterization of the Black Soldier Fly Gut Microbiome Reveals a Large Proportion of Culturable Bacteria with Potential for Industrial Applications

2021 ◽  
Vol 9 (8) ◽  
pp. 1642
Author(s):  
Dorothee Tegtmeier ◽  
Sabine Hurka ◽  
Sanja Mihajlovic ◽  
Maren Bodenschatz ◽  
Stephanie Schlimbach ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Industrial Applications ◽  
Culture Collection ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Culturable Bacteria ◽  
Black Soldier Fly ◽  
Culture Independent ◽  
Culture Dependent

Black soldier fly larvae (BSFL) are fast-growing, resilient insects that can break down a variety of organic substrates and convert them into valuable proteins and lipids for applications in the feed industry. Decomposition is mediated by an abundant and versatile gut microbiome, which has been studied for more than a decade. However, little is known about the phylogeny, properties and functions of bacterial isolates from the BSFL gut. We therefore characterized the BSFL gut microbiome in detail, evaluating bacterial diversity by culture-dependent methods and amplicon sequencing of the 16S rRNA gene. Redundant strains were identified by genomic fingerprinting and 105 non-redundant isolates were then tested for their ability to inhibit pathogens. We cultivated representatives of 26 genera, covering 47% of the families and 33% of the genera detected by amplicon sequencing. Among these isolates, we found several representatives of the most abundant genera: Morganella, Enterococcus, Proteus and Providencia. We also isolated diverse members of the less-abundant phylum Actinobacteria, and a novel genus of the order Clostridiales. We found that 15 of the isolates inhibited at least one of the tested pathogens, suggesting a role in helping to prevent colonization by pathogens in the gut. The resulting culture collection of unique BSFL gut bacteria provides a promising resource for multiple industrial applications.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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 Bacteria from the Genus Arcobacter Are Abundant in Effluent from Wastewater Treatment Plants

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Jannie Munk Kristensen ◽  
Marta Nierychlo ◽  
Mads Albertsen ◽  
Per Halkjær Nielsen
Keyword(s):  
Wastewater Treatment ◽  
Pathogenic Bacteria ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Effluent Quality ◽  
Culture Independent ◽  
Influent Wastewater

ABSTRACT Pathogenic bacteria in wastewater are generally considered to be efficiently removed in biological wastewater treatment plants. This understanding is almost solely based on culture-based control measures, and here we show, by applying culture-independent methods, that the removal of species in the genus Arcobacter was less effective than for many other abundant genera in the influent wastewater. Arcobacter was one of the most abundant genera in influent wastewater at 14 municipal wastewater treatment plants and was also abundant in the “clean” effluent from all the plants, reaching up to 30% of all bacteria as analyzed by 16S rRNA gene amplicon sequencing. Metagenomic analyses, culturing, genome sequencing of Arcobacter isolates, and visualization by fluorescent in situ hybridization (FISH) confirmed the presence of the human-pathogenic Arcobacter cryaerophilus and A. butzleri in both influent and effluent. The main reason for the high relative abundance in the effluent was probably that Arcobacter cells, compared to those of other abundant genera in the influent, did not flocculate and attach well to the activated sludge flocs, leaving a relatively large fraction dispersed in the water phase. The study shows there is an urgent need for new standardized culture-independent measurements of pathogens in effluent wastewaters, e.g., amplicon sequencing, and an investigation of the problem on a global scale to quantify the risk for humans and livestock. IMPORTANCE The genus Arcobacter was unexpectedly abundant in the effluent from 14 Danish wastewater treatment plants treating municipal wastewater, and the species included the human-pathogenic A. cryaerophilus and A. butzleri. Recent studies have shown that Arcobacter is common in wastewater worldwide, so the study indicates that discharge of members of the genus Arcobacter may be a global problem, and further studies are needed to quantify the risk and potentially minimize the discharge. The study also shows that culture-based analyses are insufficient for proper effluent quality control, and new standardized culture-independent measurements of effluent quality encompassing most pathogens should be considered.

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

scholarly journals Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

2013 ◽  
Vol 80 (1) ◽  
pp. 29-42 ◽  
Author(s):  
Jing Huang ◽  
Xia-Fang Sheng ◽  
Jun Xi ◽  
Lin-Yan He ◽  
Zhi Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Community Structure ◽  
Culture Media ◽  
Soil Formation ◽  
Mineral Weathering ◽  
Soil Profiles ◽  
Community Structures ◽  
Highly Effective ◽  
Bacterial Groups ◽  
Weathering Process

ABSTRACTBacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure.

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 Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

2020 ◽  
Author(s):  
Ezequiel Santillan ◽  
Hari Seshan ◽  
Stefan Wuertz
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Treatment Plant ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Batch Reactors ◽  
Function Structure ◽  
Community Function ◽  
And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

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.

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