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

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.

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Living Lithic and Sublithic Bacterial Communities in Namibian Drylands

Microorganisms ◽

10.3390/microorganisms9020235 ◽

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.

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Is bacterial microbiome from the Polemonium caeruleum L. (Polemoniaceae) nectar geographically variable?

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3626 ◽

2019 ◽

Vol 88 (2) ◽

Cited By ~ 1

Author(s):

Justyna Ryniewicz ◽

Przemyslaw Decewicz ◽

Lukasz Dziewit ◽

Marcin Zych

Keyword(s):

Plant Species ◽

Reproductive System ◽

Bacterial Communities ◽

Natural Populations ◽

Taxonomic Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Mixed Mating ◽

Floral Nectar ◽

Culture Independent

Floral nectar is one of the key rewards in the mutualistic interactions between plants and pollinators. However, there is a growing amount of evidence that shows that another group of organisms may be involved in the pollination process, namely the microorganisms, which often inhabit floral nectar. However, little is known about the function and taxonomic diversity of microorganisms inhabiting the nectar of plants. Bacterial communities inhabiting nectar of a rare plant species, Polemonium caeruleum, in one artificial and two natural populations in Poland were analyzed using a metagenomic approach. Polemonium caeruleum is a boreal plant species, and requires appropriate pollinator services for seed production. The reproductive system of this plant may vary between individuals and populations (mixed-mating), as well as with insect visitor assemblages. We considered that nectar-dwelling bacteria of P. caeruleum might affect the insects visiting the plant’s flowers, which in turn can result in changes in the plant’s phenotype and its reproductive system. Bacterial diversity in nectar samples was surveyed using culture-independent 16S rRNA gene amplicon sequencing (MiSeq, Illumina). We found that bacterial communities inhabiting the nectar of P. caeruleum differed between populations, although those differences were mostly quantitative. Many of the identified bacterial genera have been found previously in nectar of other plant species, or in the guts of insect visitors, and are described as tolerant of high sugar concentrations and catalase positive (which allows bacteria to survive in the presence of hydrogen peroxide).

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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

Microorganisms ◽

10.3390/microorganisms9081642 ◽

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.03044-19 ◽

2020 ◽

Vol 86 (9) ◽

Cited By ~ 5

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.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.645174 ◽

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.

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

10.1101/770354 ◽

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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Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays

Microorganisms ◽

10.3390/microorganisms10010161 ◽

2022 ◽

Vol 10 (1) ◽

pp. 161

Author(s):

Markella Tsigkrimani ◽

Magdalini Bakogianni ◽

Spiros Paramithiotis ◽

Loulouda Bosnea ◽

Eleni Pappa ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

Microbial Communities ◽

Carbon Sources ◽

Rrna Gene ◽

Ripening Stage ◽

Biolog Ecoplates ◽

Feta Cheese ◽

Main Carbon Source ◽

Early Ripening

Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep’s milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep’s milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.

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16S rRNA Gene Amplicon Sequencing of Microbial Communities Involved in Anaerobic Bulking in a Mesophilic Expanded Granular Sludge Bed Reactor Treating Wastewater Discharged from a Japanese-Style Thickened Worcestershire Sauce-Producing Factory

Microbiology Resource Announcements ◽

10.1128/mra.00801-19 ◽

2019 ◽

Vol 8 (36) ◽

Cited By ~ 1

Author(s):

Takeshi Yamada ◽

Jun Harada ◽

Yuki Okazaki ◽

Tsuyoshi Yamaguchi ◽

Atsushi Nakano

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Granular Sludge ◽

Amplicon Sequencing ◽

Organic Content ◽

Rrna Gene ◽

Sludge Bulking ◽

High Organic Content

We analyzed the prokaryotes in bulking and healthy sludge from a mesophilic expanded granular sludge bed reactor treating wastewater with high organic content by 16S rRNA gene amplicon sequencing. We tabulated the microbiota at the phylum level, providing a framework for avoiding sludge bulking.

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Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

ISME Communications ◽

10.1038/s43705-021-00077-1 ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Pengfan Zhang ◽

Stjin Spaepen ◽

Yang Bai ◽

Stephane Hacquard ◽

Ruben Garrido-Oter

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Polymorphic Variation ◽

Sequencing Data ◽

Sequencing Errors ◽

Extensive Evaluation ◽

Culture Independent ◽

Reference Sequences ◽

Synthetic Microbial Communities

AbstractSynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.

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