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Kong J, Feng J, Sun L, Zhang S. Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota. Microbiol Spectr 2023; 11:e0404822. [PMID: 37074190 PMCID: PMC10269476 DOI: 10.1128/spectrum.04048-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/24/2023] [Indexed: 04/20/2023] Open
Abstract
Benefiting from the rapid developments and wide applications of high-throughput sequencing, great advancements have been made in investigating microbiota, which are highly diverse and play key roles in both element cycling and the energy flow of ecosystems. There have been inherent limitations of amplicon sequencing that could introduce uncertainty and raise concerns about the accuracy and reproducibility of this technology. However, studies focusing on the reproducibility of amplicon sequencing are limited, especially in characterizing microbial communities in deep-sea sediments. To evaluate reproducibility, 118 deep-sea sediment samples were used for 16S rRNA gene sequencing in technical replicates (repeated measurements of the same sample) that demonstrate the variability of amplicon sequencing. The average occurrence-based overlaps were 35.98% and 27.02% between two and among three technical replicates, respectively, whereas their abundance-based overlaps reached 84.88% and 83.16%, respectively. Although variations of alpha and beta diversity indices were found between/among technical replicates, alpha diversity indices were similar across samples, and the average beta diversity indices were much smaller for technical replicates than among samples. Moreover, clustering methods (i.e., operational taxonomic units [OTUs] and amplicon sequence variants [ASVs]) were shown to have little impact on the alpha and beta diversity patterns of microbial communities. Taken together, although there are variations between/among technical replicates, amplicon sequencing is still a powerful tool with which to reveal diversity patterns of microbiota in deep-sea sediments. IMPORTANCE The reproducibility of amplicon sequencing is vital for whether the diversities of microbial communities could be accurately estimated. Thus, reproducibility influences the drawing of sound ecological conclusions. Nevertheless, few studies have focused on the reproducibility of microbial communities that are characterized by amplicon sequencing, and studies focusing on microbiota in deep-sea sediments have been especially lacking. In this study, we evaluated the reproducibility of amplicon sequencing targeting microbiota in deep-sea sediments of cold seep. Our results revealed that there were variations between/among technical replicates and that amplicon sequencing was still a powerful tool with which to characterize the diversities of microbial communities in deep-sea sediments. This study provides valuable guidelines for the reproducibility evaluation of future work in experimental design and interpretation.
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Affiliation(s)
- Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, China
| | - Jingchun Feng
- Guangdong University of Technology, Guangzhou, China
| | - Liwei Sun
- Guangdong University of Technology, Guangzhou, China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, China
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2
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Wang Z, Jimenez-Fernandez O, Osenbrück K, Schwientek M, Schloter M, Fleckenstein JH, Lueders T. Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange. WATER RESEARCH 2022; 217:118334. [PMID: 35397370 DOI: 10.1016/j.watres.2022.118334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.
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Affiliation(s)
- Zhe Wang
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany; Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany; School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Oscar Jimenez-Fernandez
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany; Department of Hydrogeology, Helmholtz-Zentrum für Umweltforschung GmbH - UFZ, Leipzig, Germany
| | - Karsten Osenbrück
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Marc Schwientek
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Michael Schloter
- Chair of Soil Science, Technical University of Munich, Freising, Germany; Research Unit for Comparative Microbiome Analyses, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Jan H Fleckenstein
- Department of Hydrogeology, Helmholtz-Zentrum für Umweltforschung GmbH - UFZ, Leipzig, Germany; Hydrologic Modelling Unit, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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3
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Nematodes As Soil Stress Indicators for Polycyclic Aromatic Hydrocarbons: a Review. Helminthologia 2022; 59:117-126. [PMID: 36118368 PMCID: PMC9444203 DOI: 10.2478/helm-2022-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/27/2022] [Indexed: 11/21/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are an important group of organic pollutants present in all parts of the environment, affecting ecosystems and human health. PAHs, which have a strong affinity for organic carbon, are found in large quantities in soil, which is one of the most important sinks for these contaminants. Their impact on the soil biotic compartments depends on a number of different factors in combination with PAH behaviour and can be assessed using soil monitoring. Soil fauna have already shown excellent properties for biomonitoring of contaminants with most promising indicator frameworks based on nematodes, which are involved in essential processes in this environment. Nematodes respond to PAHs at multiple levels, including molecular, individual and community levels. At the molecular level, this is associated with activation of metabolic pathways for xenobiotics and increased demand for energy and resources. At the individual level, this is reflected in the slowing down of various physiological processes, which has consequences at the individual and community level for sensitive taxa. In this review, the toxicity and the direct and indirect effects of PAHs on soil nematode communities are discussed. It also considers the perspectives and challenges in assessing the toxicity of PAHs and their indication using soil nematodes.
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4
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Fillinger L, Hürkamp K, Stumpp C, Weber N, Forster D, Hausmann B, Schultz L, Griebler C. Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow. Front Microbiol 2021; 12:781904. [PMID: 34912321 PMCID: PMC8667604 DOI: 10.3389/fmicb.2021.781904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.
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Affiliation(s)
- Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Kerstin Hürkamp
- Institute of Radiation Medicine, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christine Stumpp
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nina Weber
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dominik Forster
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Lotta Schultz
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
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5
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Fillinger L, Hug K, Griebler C. Aquifer recharge viewed through the lens of microbial community ecology: Initial disturbance response, and impacts of species sorting versus mass effects on microbial community assembly in groundwater during riverbank filtration. WATER RESEARCH 2021; 189:116631. [PMID: 33217664 DOI: 10.1016/j.watres.2020.116631] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Riverbank filtration has gained increasing importance for balancing rising groundwater demands and securing drinking water supplies. While microbial communities are the pillar of vital ecosystem functions in groundwater, the impact of riverbank filtration on these communities has been understudied so far. Here, we followed changes in microbial community composition based on 16S rRNA gene amplicon sequence variants (ASVs) in an initially pristine shallow porous aquifer in response to surface water intrusion during the early stages of induced riverbank filtration over a course of seven weeks. We further analyzed sediment cores for imprints of river-derived ASVs after seven weeks of riverbank filtration. The onset of the surface water intrusion caused loss of taxa and significant changes in community composition, revealing low disturbance resistance of the initial aquifer microbial communities. SourceTracker analysis revealed that proportions of river-derived ASVs in the groundwater were generally <25%, but locally could reach up to 62% during a period of intense precipitation. However, variation partitioning showed that the impact of dispersal of river-derived ASVs on changes in aquifer microbial community composition was overall outweighed by species sorting due to changes in environmental conditions caused by the infiltrating river water. Proportions of river-derived ASVs on aquifer sediments were <0.5%, showing that taxa transported from the river into the aquifer over the course of the study mainly resided as planktonic microorganisms in the groundwater. Our study demonstrates that groundwater microbial communities react sensitively to changes in environmental conditions caused by surface water intrusion, whereas mass effects resulting from the influx of river-derived taxa play a comparatively minor role.
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Affiliation(s)
- Lucas Fillinger
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Katrin Hug
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Christian Griebler
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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6
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Klatt JM, Gomez-Saez GV, Meyer S, Ristova PP, Yilmaz P, Granitsiotis MS, Macalady JL, Lavik G, Polerecky L, Bühring SI. Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat. THE ISME JOURNAL 2020; 14:3024-3037. [PMID: 32770117 PMCID: PMC7784965 DOI: 10.1038/s41396-020-0734-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/16/2020] [Accepted: 07/28/2020] [Indexed: 11/15/2022]
Abstract
Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with sulfur reducing bacteria (SRB). Using microsensors and stable isotope probing we found that dissolved organic carbon (DOC) released by OP fuels sulfide production, likely by a specialized SRB population. Increased sulfide fluxes were only stimulated after the cyanobacteria switched from AP to OP. O2 production triggered migration of large sulfur-oxidizing bacteria from the surface to underneath the cyanobacterial layer. The resultant sulfide shield tempered AP and allowed OP to occur for a longer duration over a diel cycle. The lack of cyanobacterial DOC supply to SRB during AP therefore maximized O2 export. This mechanism is unique to benthic ecosystems because transitions between metabolisms occur on the same time scale as solute transport to functionally distinct layers, with the rearrangement of the system by migration of microorganisms exaggerating the effect. Overall, cyanobacterial versatility disrupts the synergistic relationship between sulfide production and AP, and thus enhances diel O2 production.
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Affiliation(s)
- Judith M Klatt
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
- Alfred Wegener Institute-Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
| | - Steffi Meyer
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Thünen Institute of Baltic Sea Fisheries, Thünen Institute, Rostock, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
| | - Pelin Yilmaz
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael S Granitsiotis
- Research Unit Environmental Genomics, Helmholtz Zentrum Munich, Munich, Germany
- Department of Environmental Engineering, University of Patras, Agrinio, Greece
- DOE, Joint Genome Institute, Lawerence Berkeley National Lab, Berkeley, CA, USA
| | | | - Gaute Lavik
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lubos Polerecky
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Earth Sciences-Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
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7
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Hofmann R, Uhl J, Hertkorn N, Griebler C. Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments. Front Microbiol 2020; 11:543567. [PMID: 33250862 PMCID: PMC7674671 DOI: 10.3389/fmicb.2020.543567] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.
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Affiliation(s)
- Roland Hofmann
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany.,Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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8
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Zhu B, Friedrich S, Wang Z, Táncsics A, Lueders T. Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments. Front Microbiol 2020; 11:1867. [PMID: 32922372 PMCID: PMC7456981 DOI: 10.3389/fmicb.2020.01867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/16/2020] [Indexed: 01/04/2023] Open
Abstract
Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.
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Affiliation(s)
- Baoli Zhu
- Chair of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | | | - Zhe Wang
- Chair of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent Istvan University, Gödöllö, Hungary
| | - Tillmann Lueders
- Chair of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
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9
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De Vrieze J, De Mulder T, Matassa S, Zhou J, Angenent LT, Boon N, Verstraete W. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microb Biotechnol 2020; 13:829-843. [PMID: 32311222 PMCID: PMC7264747 DOI: 10.1111/1751-7915.13575] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023] Open
Abstract
Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | | | - Silvio Matassa
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Largus T Angenent
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
- Avecom NV, Industrieweg 122P, Wondelgem, 9032, Belgium
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10
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Fillinger L, Hug K, Griebler C. Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers. FEMS Microbiol Ecol 2020; 95:5584335. [PMID: 31598689 PMCID: PMC6821248 DOI: 10.1093/femsec/fiz160] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/06/2019] [Indexed: 12/21/2022] Open
Abstract
Several studies have analyzed biogeographic distribution patterns of microbial communities across broad spatial scales. However, it is often unclear to what extent differences in community composition across different regions are caused by dispersal limitation or selection, and if selection is caused by local environmental conditions alone or additional broad-scale region-specific factors. This is especially true for groundwater environments, which have been understudied in this context relative to other non-subsurface habitats. Here, we analyzed microbial community composition based on exact 16S rRNA amplicon sequence variants (ASVs) from four geographically separated aquifers located in different regions along a latitudinal transect of ∼700 km across Germany. Using a combination of variation partitioning and ecological null models revealed that differences in microbial community composition were mainly the product of selection imposed by local environmental conditions and to a smaller but still significant extent dispersal limitation and drift across regions. Only ∼23% of the total variation in microbial community composition remained unexplained, possibly due to underestimated effects of dispersal limitation among local communities within regions and temporal drift. No evidence was found for selection due to region-specific factors independent of local environmental conditions.
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Affiliation(s)
- Lucas Fillinger
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Katrin Hug
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Christian Griebler
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany.,Department of Limnology & Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
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11
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Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines. Microorganisms 2019; 8:microorganisms8010030. [PMID: 31877898 PMCID: PMC7022543 DOI: 10.3390/microorganisms8010030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.
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12
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Frank U, Kublik S, Mayer D, Engel M, Schloter M, Durner J, Gaupels F. A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing. BMC PLANT BIOLOGY 2019; 19:539. [PMID: 31801481 PMCID: PMC6894221 DOI: 10.1186/s12870-019-2162-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. RESULTS Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation. CONCLUSIONS The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
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Affiliation(s)
- Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dörte Mayer
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
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Zhu B, Wang J, Bradford LM, Ettwig K, Hu B, Lueders T. Nitric Oxide Dismutase ( nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers. Front Microbiol 2019; 10:1577. [PMID: 31354671 PMCID: PMC6636425 DOI: 10.3389/fmicb.2019.01577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.
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Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lauren M Bradford
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Ettwig
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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14
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Gut bacteria of the cowpea beetle mediate its resistance to dichlorvos and susceptibility to Lippia adoensis essential oil. Sci Rep 2019; 9:6435. [PMID: 31015559 PMCID: PMC6478711 DOI: 10.1038/s41598-019-42843-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/09/2019] [Indexed: 11/30/2022] Open
Abstract
Bacteria inhabiting the gut of insects provide many benefits to their hosts, such as aiding in food digestion, reproduction, and immunity, tissue homeostasis, adaptation to environment and resistance to pathogen and pesticides. The cowpea beetle, Callosobruchus maculatus, is a serious cosmopolitan pest of pulses. This beetle has lent itself as a guinea pig for several ecological studies. It harbors a consortium of bacterial communities in its gut, but the evidence for their role in its physiology is fragmentary. In this work, we hypothesized that gut microbiota mediates C. maculatus resistance to dichlorvos (DDVP or O,O-dimethyl O-2,2-dichlorovinylphosphate) and represent the target of Lippia adoensis (Gambian Tea Bush) essential oil (EO). Symbiotic and aposymbiotic beetles were exposed to artificial cowpea seeds earlier treated with DDVP or EO. Adult mortality and changes in gut bacterial community composition and abundance were examined at F1 and F5 generations. The susceptibility of experimental beetles to DDVP was significantly affected by their symbiotic status. The adult mortality decreased across generations in DDVP treatments, and remained significantly higher in aposymbiotic groups. In EO treatments, the mortality was consistent irrespective of symbiotic status and experimental generations. When compared to DDVP and the Control, EO treatments had significantly lower bacterial richness and diversity, as well as lower abundance of Proteobacteria, Firmicutes, and Bacteroidetes. These results support our hypothesis and describe the responses of gut microbial communities to pesticide treatments. This could be of interest for developing new management strategies of this pest.
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15
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Fredriksson NJ, Hermansson M, Wilén BM. Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant. ENVIRONMENTAL TECHNOLOGY 2019; 40:912-928. [PMID: 29187074 DOI: 10.1080/09593330.2017.1411396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.
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Affiliation(s)
- Nils Johan Fredriksson
- a Department of Architecture and Civil Engineering, Water Environment Technology , Chalmers University of Technology , Gothenburg , Sweden
| | - Malte Hermansson
- b Department of Chemistry and Molecular Biology, Microbiology , University of Gothenburg , Gothenburg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering, Water Environment Technology , Chalmers University of Technology , Gothenburg , Sweden
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16
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Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer. Microorganisms 2019; 7:microorganisms7020046. [PMID: 30744114 PMCID: PMC6406676 DOI: 10.3390/microorganisms7020046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ.
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17
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Mori F, Umezawa Y, Kondo R, Wada M. Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay. Microbes Environ 2018; 33:378-384. [PMID: 30449831 PMCID: PMC6308007 DOI: 10.1264/jsme2.me18092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
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18
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De Vrieze J, Ijaz UZ, Saunders AM, Theuerl S. Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion. Sci Rep 2018; 8:16818. [PMID: 30429514 PMCID: PMC6235954 DOI: 10.1038/s41598-018-34921-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium.
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, UK
| | - Aaron M Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngardsholmsvej 49, 9000, Aalborg, Denmark
| | - Susanne Theuerl
- Leibniz Institute for Agricultural Engineering and Bioeconomy e.V. (ATB), Department Bioengineering, Max-Eyth-Allee 100, D-14469, Potsdam, Germany
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19
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Development and testing of an 18S rRNA phylogenetic microarray for marine sediments. J Microbiol Methods 2018; 154:95-106. [DOI: 10.1016/j.mimet.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 10/08/2018] [Indexed: 11/22/2022]
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20
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Cai J, Bai C, Tang X, Dai J, Gong Y, Hu Y, Shao K, Zhou L, Gao G. Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31543-31557. [PMID: 30206827 DOI: 10.1007/s11356-018-2987-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
While the important roles of microbial communities in oceanic hypoxic zones were beginning to be understood, little is known about microbial community associated with this phenomenon in shallow lakes. To address this deficit, both the bacterial and microbial eukaryotic communities of an ephemeral hypoxic area of Taihu Lake were characterized. The hypoxia provided nutritional niches for various bacteria, which results in high abundance and diversity. Specific bacterial groups, such as vadinBC27 subgroup of Bacteroidetes, Burkholderiales, Rhodocyclales, Pseudomonas, and Parcubacteria, were dominated in hypoxic sites and relevant to the fermentation, denitrification, nitrification, and sulfur metabolism. Conversely, most of microbial eukaryotes disappeared along with the decline of DO. An unexpected dominance of fungi was observed during hypoxia, which partly explained by the accumulation of toxic algae. Mucor was the single dominant genus in the hypoxic zone. We proposed that this group might cooperate with bacterial communities in the anaerobic degradation of algal biomass and woody materials. Generally, the hypoxic microbiome in shallow lakes is mainly involved in fermentative metabolism depending on phytodetritus and is potentially influenced by terrestrial sources. This study provided new insights into the unique microbiome in short-term hypoxia in shallow lakes and lays the foundation for studies that will enhance our understanding of the microbial players associated with hypoxia and their adaption strategy on the global scale.
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Affiliation(s)
- Jian Cai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Chengrong Bai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Jiangyu Dai
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, 210029, People's Republic of China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Lei Zhou
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
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21
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Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, Kleindienst S, Schmidt C. Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples? FEMS Microbiol Ecol 2018; 94:5104375. [DOI: 10.1093/femsec/fiy189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Viktoria Soos
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Saskia Rughöft
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
- Geomicrobiology, Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
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22
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Response of Bacterial Communities upon Application of Different Innovative Organic Fertilizers in a Greenhouse Experiment Using Low-Nutrient Soil Cultivated with Cynodon dactylon. SOIL SYSTEMS 2018. [DOI: 10.3390/soilsystems2030052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Assessing the response of microbial communities to nutrient inputs in man-managed soils is of primary importance to understand the impact on ecosystem services provided by the soil microbiome. In this study, a low-nutrient soil was supplemented with seven different innovative fertilizers including matrixes of plant, animal, fungal or synthetic origin, and dosed to deliver the same amount of nitrogen. Growth of a potted grass crop (Cynodon dactylon) was recorded and the fertilizers were scored by the plant yield obtained in a greenhouse study. Soil was sampled at 9 and 58 days after the addition and bacterial community composition was analyzed after soil DNA extraction through pyrosequencing of 16S rDNA gene amplicons. Over 900 bacterial genera were detected, belonging to 21 described and 19 candidate phyla. In spite of the equal dose of nitrogen delivered, specific groups were fostered by given fertilizers; in particular marked effects on some phyla were displayed by a yeast-based fertilizer, which was also most effective in plant productivity. The main shifts were observed shortly after the fertilizer application, followed by a gradual stabilization of the equilibrium and by a rise in community evenness.
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23
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Lindström S, Rowe O, Timonen S, Sundström L, Johansson H. Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies. PeerJ 2018; 6:e5289. [PMID: 30042898 PMCID: PMC6055595 DOI: 10.7717/peerj.5289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.
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Affiliation(s)
- Stafva Lindström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Owen Rowe
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Sari Timonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Helena Johansson
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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24
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Suitability and setup of next-generation sequencing-based method for taxonomic characterization of aquatic microbial biofilm. Folia Microbiol (Praha) 2018; 64:9-17. [PMID: 29909524 DOI: 10.1007/s12223-018-0624-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/06/2018] [Indexed: 10/14/2022]
Abstract
A robust and widely applicable method for sampling of aquatic microbial biofilm and further sample processing is presented. The method is based on next-generation sequencing of V4-V5 variable regions of 16S rRNA gene and further statistical analysis of sequencing data, which could be useful not only to investigate taxonomic composition of biofilm bacterial consortia but also to assess aquatic ecosystem health. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant; however, the non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The bias of the method is assessed with respect to the employment of a non-quantitative step (PCR amplification) to obtain quantitative results (relative abundance of identified taxa). This aspect is often overlooked in ecological and medical studies. We document that sequencing of a mixture of three merged primary PCR reactions for each sample and further evaluation of median values from three technical replicates for each sample enables to overcome this bias and gives robust and repeatable results well distinguishing among sampling localities and seasons.
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25
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Táncsics A, Szalay AR, Farkas M, Benedek T, Szoboszlay S, Szabó I, Lueders T. Stable isotope probing of hypoxic toluene degradation at the Siklós aquifer reveals prominent role of Rhodocyclaceae. FEMS Microbiol Ecol 2018; 94:4995907. [PMID: 29767715 PMCID: PMC5972620 DOI: 10.1093/femsec/fiy088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 02/01/2023] Open
Abstract
The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place. A large diversity of subfamily I.2.C extradiol dioxygenase genes has been previously detected in a BTEX-contaminated aquifer in Hungary. Older literature suggests that such catabolic potentials could be associated to hypoxic degradation. Bacterial communities dominated by members of the Rhodocyclaceae were found, but the majority of the detected C23O genotypes could not be affiliated to any known bacterial degrader lineages. To address this, a stable isotope probing (SIP) incubation of site sediments with 13C7-toluene was performed under microoxic conditions. A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. The main assimilators of 13C were identified as members of the genera Quatrionicoccus and Zoogloea, and a yet uncultured group of the Rhodocyclaceae.
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Affiliation(s)
- András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Anna Róza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1., 85764 Neuherberg, Germany
| | - Milan Farkas
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - István Szabó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1., 85764 Neuherberg, Germany
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Kuppardt A, Fester T, Härtig C, Chatzinotas A. Rhizosphere Protists Change Metabolite Profiles in Zea mays. Front Microbiol 2018; 9:857. [PMID: 29780370 PMCID: PMC5946010 DOI: 10.3389/fmicb.2018.00857] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/13/2018] [Indexed: 01/16/2023] Open
Abstract
Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.
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Affiliation(s)
- Anke Kuppardt
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thomas Fester
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Claus Härtig
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Herzyk A, Fillinger L, Larentis M, Qiu S, Maloszewski P, Hünniger M, Schmidt SI, Stumpp C, Marozava S, Knappett PSK, Elsner M, Meckenstock R, Lueders T, Griebler C. Response and recovery of a pristine groundwater ecosystem impacted by toluene contamination - A meso-scale indoor aquifer experiment. JOURNAL OF CONTAMINANT HYDROLOGY 2017; 207:17-30. [PMID: 29128133 DOI: 10.1016/j.jconhyd.2017.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Microbial communities are the driving force behind the degradation of contaminants like aromatic hydrocarbons in groundwater ecosystems. However, little is known about the response of native microbial communities to contamination in pristine environments as well as their potential to recover from a contamination event. Here, we used an indoor aquifer mesocosm filled with sandy quaternary calciferous sediment that was continuously fed with pristine groundwater to study the response, resistance and resilience of microbial communities to toluene contamination over a period of almost two years, comprising 132days of toluene exposure followed by nearly 600days of recovery. We observed an unexpectedly high intrinsic potential for toluene degradation, starting within the first two weeks after the first exposure. The contamination led to a shift from oxic to anoxic, primarily nitrate-reducing conditions as well as marked cell growth inside the contaminant plume. Depth-resolved community fingerprinting revealed a low resistance of the native microbial community to the perturbation induced by the exposure to toluene. Distinct populations that were dominated by a small number of operational taxonomic units (OTUs) rapidly emerged inside the plume and at the plume fringes, partially replacing the original community. During the recovery period physico-chemical conditions were restored to the pristine state within about 35days, whereas the recovery of the biological parameters was much slower and the community composition inside the former plume area had not recovered to the original state by the end of the experiment. These results demonstrate the low resilience of sediment-associated groundwater microbial communities to organic pollution and underline that recovery of groundwater ecosystems cannot be assessed solely by physico-chemical parameters.
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Affiliation(s)
- Agnieszka Herzyk
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Lucas Fillinger
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Michael Larentis
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Shiran Qiu
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Piotr Maloszewski
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Marko Hünniger
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Susanne I Schmidt
- University of Koblenz-Landau, Institute for Environmental Sciences, Landau, Germany
| | - Christine Stumpp
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Sviatlana Marozava
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Peter S K Knappett
- Texas A&M University, College of Geosciences, Department of Geology & Geophysics, College Station, Texas, United States
| | - Martin Elsner
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany; Technical University of Munich, Chair of Analytical Chemistry and Water Chemistry, Munich, Germany
| | - Rainer Meckenstock
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany; University of Duisburg-Essen, Biofilm Centre, Aquatic Microbiology, Essen, Germany
| | - Tillmann Lueders
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany
| | - Christian Griebler
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Neuherberg, Germany.
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Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture. Biodegradation 2017; 29:23-39. [PMID: 29177812 PMCID: PMC5773621 DOI: 10.1007/s10532-017-9811-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/02/2017] [Indexed: 11/13/2022]
Abstract
An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)3 as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a 13C-carbon label from 13C10-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.
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Epelde L, Lanzén A, Mijangos I, Sarrionandia E, Anza M, Garbisu C. Short-term effects of non-grazing on plants, soil biota and aboveground-belowground links in Atlantic mountain grasslands. Sci Rep 2017; 7:15097. [PMID: 29118337 PMCID: PMC5678074 DOI: 10.1038/s41598-017-15345-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022] Open
Abstract
Mountain grasslands in the Iberian Peninsula are the result of extensive grazing. However, a progressive abandonment of grazing activity is currently observed in the study region. The objective of this work was to evaluate the short-term (2 years) effects of non-grazing on the diversity and composition of plants, soil microorganisms (prokaryotes, fungi, arbuscular mycorrhiza), mesofauna, macrofauna and aboveground-belowground links, through the study of 16 grazed vs. non-grazed areas in Atlantic grasslands located in the Basque Country (Spain). Sites were divided between 4 habitat types with different elevation, pasture productivity, vegetation type and parent material. Herbivores appeared to influence plant community composition, contributing to increase aboveground diversity, while having unequal effects on belowground communities depending on the organisms analysed. This may be explained by the different habitat and trophic level of each soil organism, which may be more or less affected by the predominating negative effects of grazing, such as soil compaction, and only partially compensated by other positive effects. Finally, habitat type appeared to be the strongest influence on both above- and belowground communities, also influencing the effect of the absence of grazing.
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Affiliation(s)
- Lur Epelde
- NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Department of Conservation of Natural Resources, c/Berreaga 1, E-48160, Derio, Spain.
| | - Anders Lanzén
- NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Department of Conservation of Natural Resources, c/Berreaga 1, E-48160, Derio, Spain
| | - Iker Mijangos
- NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Department of Conservation of Natural Resources, c/Berreaga 1, E-48160, Derio, Spain
| | - Estibaliz Sarrionandia
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-01006, Vitoria, Gasteiz, Spain
| | - Mikel Anza
- NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Department of Conservation of Natural Resources, c/Berreaga 1, E-48160, Derio, Spain
| | - Carlos Garbisu
- NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Department of Conservation of Natural Resources, c/Berreaga 1, E-48160, Derio, Spain
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Karwautz C, Kus G, Stöckl M, Neu TR, Lueders T. Microbial megacities fueled by methane oxidation in a mineral spring cave. ISME JOURNAL 2017; 12:87-100. [PMID: 28949325 PMCID: PMC5739006 DOI: 10.1038/ismej.2017.146] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000 p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.
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Affiliation(s)
- Clemens Karwautz
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Günter Kus
- Bavarian Environment Agency (LfU), Department 10: Geological Survey, Hof/Saale, Germany
| | - Michael Stöckl
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Magdeburg, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
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31
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Cardinale M, Kaiser D, Lueders T, Schnell S, Egert M. Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species. Sci Rep 2017; 7:5791. [PMID: 28725026 PMCID: PMC5517580 DOI: 10.1038/s41598-017-06055-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/07/2017] [Indexed: 12/22/2022] Open
Abstract
The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454–pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH–CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH–CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm–like structures occurred. Image analysis showed local densities of up to 5.4 * 1010 cells per cm3, and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Dominik Kaiser
- Faculty of Medical and Life Sciences, Institute of Precision Medicine (IPM), Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine (IPM), Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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32
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Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments. PLoS One 2017. [PMID: 28622351 PMCID: PMC5473592 DOI: 10.1371/journal.pone.0179443] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a “sufficient” replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.
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Affiliation(s)
- Anders Lanzén
- NEIKER-Tecnalia, Department of Conservation of Natural Resources, Bizkaia Technology Park, Derio, Spain
- * E-mail:
| | - Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eric M. Thompson
- Department of Biology, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Uni Research Environment, Uni Research AS, Bergen, Norway
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Zhu B, Bradford L, Huang S, Szalay A, Leix C, Weissbach M, Táncsics A, Drewes JE, Lueders T. Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems. Appl Environ Microbiol 2017; 83:e02750-16. [PMID: 27986721 PMCID: PMC5288823 DOI: 10.1128/aem.02750-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/02/2016] [Indexed: 11/20/2022] Open
Abstract
It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g-1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. IMPORTANCE NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium "Ca Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.
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Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Lauren Bradford
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Sichao Huang
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Anna Szalay
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Carmen Leix
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Max Weissbach
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | | | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
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Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology 2017; 98:555-564. [DOI: 10.1002/ecy.1670] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/09/2016] [Accepted: 11/17/2016] [Indexed: 11/07/2022]
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Mauffret A, Baran N, Joulian C. Effect of pesticides and metabolites on groundwater bacterial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 576:879-887. [PMID: 27838578 DOI: 10.1016/j.scitotenv.2016.10.108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
We assessed the effect of pesticides, especially commonly detected herbicides, on bacterial communities in groundwater. To this end, we used a combined approach with i) triazine-spiked experiments at environmentally relevant concentrations (1 and 10μg/L) in waters with contrasting contamination histories, and ii) in situ monitoring in a rural aquifer, where many additional biotic and abiotic parameters also affect the community. Microbial community was characterized by fingerprinting techniques (CE-SSCP), gene presence (atzA/B/C/D/E/F and amoA genes) and abundance (16S RNA, napA and narG genes). During triazine-spiked experiments, the bacterial community structure in reference water was modified following an exposure to atrazine (ATZ) and/or its metabolite desethylatrazine (DEA) at 1μg/L; in historically-contaminated water, the bacterial community structure was modified following an exposure to 10μg/L ATZ/DEA. Similarly, biodiversity indices and biomass in the reference water appeared affected at lower triazine concentrations than in the historically-contaminated water, though these end-points are less sensitive than the community structure. Our results thus suggest that the history of contamination induced a community tolerance to the tested triazines. ATZ and DEA were not degraded during the experiment and this was consistent with the absence of atz genes involved in their degradation in none of the tested conditions. In field monitoring, triazines that represent a historical and diffuse contamination of groundwater, participate in the microbial community structure, confirming the triazine effect observed under laboratory conditions. Other herbicides, such as chloroacetanilides that are applied today, did not appear to affect the whole community structure; they however induced a slight, but significant, increase in the abundance of nitrate-reducing bacteria. To our best knowledge, this is the first study on the microbial ecotoxicology of pesticides and their metabolites at environmentally relevant concentrations in groundwater.
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Affiliation(s)
| | - Nicole Baran
- The French Geological Survey (BRGM), Orléans, France
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36
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Dubey G, Kollah B, Gour VK, Shukla AK, Mohanty SR. Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas. 3 Biotech 2016; 6:257. [PMID: 28330329 PMCID: PMC5135702 DOI: 10.1007/s13205-016-0546-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/11/2016] [Indexed: 11/29/2022] Open
Abstract
Plant-microbial interaction in rhizosphere plays vital role in shaping plant’s growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties. Diversity was estimated by terminal restriction fragment length polymorphism (TRFLP) targeting 16S rRNA gene of bacteria and archaea. Fifteen bacterial and 17 archaeal terminal restriction fragments (TRFs) were retrieved from J. curcas rhizosphere. Bacterial indicative TRFs were Actinobacteria, Firmicutes, Acidobacteria, Verrumicrobiaceae, and Chlroflexi. Major archaeal TRFs were crenarchaeota, and euryarchaeota. In case of bacteria, relative fluorescence was low for TRF160 and high for TRF51, TRF 420. Similarly, for archaea relative fluorescence of TRF 218, and TRF 282 was low and high for TRF 278, TRF468 and TRF93. Principal component analysis (PCA) of bacterial TRFs designated PC 1 with 46.83% of variation and PC2 with 31.07% variation. Archaeal TRFs designated 90.94% of variation by PC1 and 9.05% by PC2. Simpson index varied from 0.530 to 0.880 and Shannon index from 1.462 to 3.139 for bacteria. For archaea, Simpson index varied from 0.855 to 0.897 and Shannon index varied from 3.027 to 3.155. Study concluded that rhizosphere of J. curcas constituted of diverse set of both bacteria and archaea, which might have promising plant growth promoting activities.
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Affiliation(s)
- Garima Dubey
- Indian Institute of Soil Science, Nabibagh, Bhopal, 462038, India
| | - Bharati Kollah
- Indian Institute of Soil Science, Nabibagh, Bhopal, 462038, India
| | - Vijay Kumar Gour
- Department of Plant Breeding and Genetics, J.N. Agricultural University, Krishinagar, Jabalpur, 482004, India
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An X, Baker P, Li H, Su J, Yu C, Cai C. The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:21766-21779. [PMID: 27522211 DOI: 10.1007/s11356-016-7381-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO42- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.
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Affiliation(s)
- Xinli An
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Paul Baker
- Bangor University, Bangor, Gwynedd, LL572DG, UK
| | - Hu Li
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqiang Su
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Changping Yu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chao Cai
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Kramer S, Dibbern D, Moll J, Huenninghaus M, Koller R, Krueger D, Marhan S, Urich T, Wubet T, Bonkowski M, Buscot F, Lueders T, Kandeler E. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil. Front Microbiol 2016; 7:1524. [PMID: 27725815 PMCID: PMC5035733 DOI: 10.3389/fmicb.2016.01524] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/12/2016] [Indexed: 01/31/2023] Open
Abstract
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
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Affiliation(s)
- Susanne Kramer
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Dörte Dibbern
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany
| | - Maike Huenninghaus
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Robert Koller
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Dirk Krueger
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle Halle, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Tim Urich
- Department of Bacterial Physiology, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald Greifswald, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
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Badin A, Broholm MM, Jacobsen CS, Palau J, Dennis P, Hunkeler D. Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools. JOURNAL OF CONTAMINANT HYDROLOGY 2016; 192:1-19. [PMID: 27318432 DOI: 10.1016/j.jconhyd.2016.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/06/2016] [Accepted: 05/17/2016] [Indexed: 06/06/2023]
Abstract
Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C-Cl isotope analysis together with the almost absent VC (13)C depletion in comparison to cDCE (13)C depletion suggested that cDCE was subject to abiotic degradation due to the presence of pyrite, possible surface-bound iron (II) or reduced iron sulphides in the downgradient part of the plume. This interpretation is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more reduced redox conditions which favor active reductive dechlorination and/or may lead to a series of redox reactions which may consecutively trigger biotically induced abiotic degradation. Finally, this study illustrates the valuable complementary application of compound-specific isotopic analysis combined with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes.
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Affiliation(s)
- Alice Badin
- University of Neuchâtel, Centre for Hydrogeology & Geothermics (CHYN), Rue Emile Argand 11, CH 2000 Neuchâtel, Switzerland
| | - Mette M Broholm
- Technical University of Denmark (DTU), Department of Environmental Engineering, Miljøvej, DTU B113, DK 2800 Kgs. Lyngby, Denmark
| | - Carsten S Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Ø. Voldgade 10, 1350 København K, Denmark
| | - Jordi Palau
- University of Neuchâtel, Centre for Hydrogeology & Geothermics (CHYN), Rue Emile Argand 11, CH 2000 Neuchâtel, Switzerland
| | - Philip Dennis
- SiREM, 130 Research Lane, Guelph, Ontario, N1G5G3, Canada
| | - Daniel Hunkeler
- University of Neuchâtel, Centre for Hydrogeology & Geothermics (CHYN), Rue Emile Argand 11, CH 2000 Neuchâtel, Switzerland
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Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Mol Ecol 2016; 25:4392-406. [DOI: 10.1111/mec.13761] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Anders Lanzén
- Department of Conservation of Natural Resources; NEIKER Tecnalia; Bizkaia Technology Park 48160 Derio Spain
| | - Katrine Lekang
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
| | - Inge Jonassen
- Computational Biology Unit; Department of Informatics; University of Bergen; Bergen Norway
| | - Eric M. Thompson
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
- Sars International Centre for Marine Molecular Biology; University of Bergen; Bergen Norway
- Uni Research Environment; Uni Research AS; 5020 Bergen Norway
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Kocur CMD, Lomheim L, Molenda O, Weber KP, Austrins LM, Sleep BE, Boparai HK, Edwards EA, O'Carroll DM. Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:7658-7670. [PMID: 27305345 DOI: 10.1021/acs.est.6b01745] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.
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Affiliation(s)
- Chris M D Kocur
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Line Lomheim
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Olivia Molenda
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Kela P Weber
- Environmental Sciences Group, Chemistry and Chemical Engineering, Royal Military College of Canada , PO Box 17000, Station Forces, Kingston, Ontario, Canada , K7K 7B4
| | - Leanne M Austrins
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Brent E Sleep
- Civil Engineering, University of Toronto , 35 Saint George Street, Toronto, Ontario, Canada , M5S 1A4
| | - Hardiljeet K Boparai
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
| | - Elizabeth A Edwards
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Denis M O'Carroll
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
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Gschwendtner S, Mansfeldt T, Kublik S, Touliari E, Buegger F, Schloter M. Long-term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide-derived carbon in soil. Microb Biotechnol 2016; 9:502-13. [PMID: 27194597 PMCID: PMC4919992 DOI: 10.1111/1751-7915.12362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/18/2016] [Accepted: 03/28/2016] [Indexed: 11/28/2022] Open
Abstract
Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source.
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Affiliation(s)
- Silvia Gschwendtner
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Tim Mansfeldt
- Department Geowissenschaften, Bodengeographie/Bodenkunde, Universität zu Köln, Albertus-Magnus-Platz, Köln, 50923, Germany
| | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Evangelia Touliari
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
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Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning. Extremophiles 2016; 20:795-808. [DOI: 10.1007/s00792-016-0855-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/14/2016] [Indexed: 01/23/2023]
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Lanzén A, Epelde L, Blanco F, Martín I, Artetxe U, Garbisu C. Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient. Sci Rep 2016; 6:28257. [PMID: 27321429 PMCID: PMC4913321 DOI: 10.1038/srep28257] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/01/2016] [Indexed: 11/09/2022] Open
Abstract
Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.
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Affiliation(s)
- Anders Lanzén
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Lur Epelde
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Fernando Blanco
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Iker Martín
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Unai Artetxe
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Carlos Garbisu
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
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Strandh M, Råberg L. Within-host competition between Borrelia afzelii ospC strains in wild hosts as revealed by massively parallel amplicon sequencing. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0293. [PMID: 26150659 DOI: 10.1098/rstb.2014.0293] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Infections frequently consist of more than one strain of a given pathogen. Experiments have shown that co-infecting strains often compete, so that the infection intensity of each strain in mixed infections is lower than in single strain infections. Such within-host competition can have important epidemiological and evolutionary consequences. However, the extent of competition has rarely been investigated in wild, naturally infected hosts, where there is noise in the form of varying inoculation doses, asynchronous infections and host heterogeneity, which can potentially alleviate or eliminate competition. Here, we investigated the extent of competition between Borrelia afzelii strains (as determined by ospC genotype) in three host species sampled in the wild. For this purpose, we developed a protocol for 454 amplicon sequencing of ospC, which allows both detection and quantification of each individual strain in an infection. Each host individual was infected with one to six ospC strains. The infection intensity of each strain was lower in mixed infections than in single ones, showing that there was competition. Rank-abundance plots revealed that there was typically one dominant strain, but that the evenness of the relative infection intensity of the different strains in an infection increased with the multiplicity of infection. We conclude that within-host competition can play an important role under natural conditions despite many potential sources of noise, and that quantification by next-generation amplicon sequencing offers new possibilities to dissect within-host interactions in naturally infected hosts.
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Affiliation(s)
- Maria Strandh
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Lars Råberg
- Functional Zoology, Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
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Barnes CJ, van der Gast CJ, Burns CA, McNamara NP, Bending GD. Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities. Front Microbiol 2016; 7:195. [PMID: 26941720 PMCID: PMC4766365 DOI: 10.3389/fmicb.2016.00195] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/05/2015] [Indexed: 11/16/2022] Open
Abstract
Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.
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Affiliation(s)
- Christopher J. Barnes
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
- Section of Evolutionary Genomics, National History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | | | - Caitlin A. Burns
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
| | - Niall P. McNamara
- Natural Environment Research Council Centre for Ecology and Hydrology – Lancaster Environment CentreLancaster, UK
| | - Gary D. Bending
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
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47
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Changes in bacterial community structure in a full-scale membrane bioreactor for municipal wastewater treatment. J Biosci Bioeng 2016; 122:97-104. [PMID: 26811223 DOI: 10.1016/j.jbiosc.2015.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 11/23/2022]
Abstract
This study investigated changes in the structure and metabolic capabilities of the bacterial community in a full-scale membrane bioreactor (MBR) treating municipal wastewater. Microbial monitoring was also conducted for a parallel-running conventional activated sludge (CAS) process treating the same influent. The mixed-liquor suspended solid concentration in the MBR reached a steady-state on day 73 after the start-up. Then the MBR maintained higher rates of removal of organic compounds and nitrogen than the CAS process did. Terminal restriction fragment length polymorphism analysis revealed that the bacterial community structure in the MBR was similar to that in the CAS process at the start-up, but it became very different from that in the CAS process in the steady state. The bacterial community structure of the MBR continued to change dynamically even after 20 months of the steady-state operation, while that of the CAS process was maintained in a stable condition. By contrast, Biolog assay revealed that the carbon source utilization potential of the MBR resembled that of the CAS process as a whole, although it declined transiently. Overall, the results indicate that the bacterial community of the MBR has flexibility in terms of its phylogenetic structure and metabolic activity to maintain the high wastewater treatment capability.
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Pasulka AL, Levin LA, Steele JA, Case DH, Landry MR, Orphan VJ. Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem. Environ Microbiol 2016; 18:3022-43. [PMID: 26663587 DOI: 10.1111/1462-2920.13185] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/03/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.
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Affiliation(s)
- Alexis L Pasulka
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Lisa A Levin
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Josh A Steele
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - David H Case
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Michael R Landry
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs. PLoS One 2016; 11:e0144702. [PMID: 26788724 PMCID: PMC4720286 DOI: 10.1371/journal.pone.0144702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/23/2015] [Indexed: 12/28/2022] Open
Abstract
Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.
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Chakravorty S, Bhattacharya S, Chatzinotas A, Chakraborty W, Bhattacharya D, Gachhui R. Kombucha tea fermentation: Microbial and biochemical dynamics. Int J Food Microbiol 2016; 220:63-72. [PMID: 26796581 DOI: 10.1016/j.ijfoodmicro.2015.12.015] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 12/24/2015] [Accepted: 12/31/2015] [Indexed: 11/18/2022]
Abstract
Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our data thus indicate that the microbial community structure and dynamics play an important role in the biochemistry of the fermentation of the beverage. We envisage that combined molecular and biochemical analyses like in our study will provide valuable insights for better understanding the role of the microbial community for the beneficial properties of the beverage.
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Affiliation(s)
- Somnath Chakravorty
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Semantee Bhattacharya
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Writachit Chakraborty
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Debanjana Bhattacharya
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Ratan Gachhui
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India.
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