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Varsadiya M, Urich T, Hugelius G, Bárta J. Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic. FEMS Microbiol Ecol 2021; 97:6102547. [PMID: 33452882 DOI: 10.1093/femsec/fiab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 01/12/2023] Open
Abstract
Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens - mcrA gene and diazotrophs - nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.
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Affiliation(s)
- Milan Varsadiya
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8 17487 Greifswald, Germany
| | - Gustaf Hugelius
- Department of Physical Geography, Stockholm University, 106 91, Stockholm, Sweden
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
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Zhou Z, Tao Y, Zhang S, Xiao Y, Meng F, Stuckey DC. Size-dependent microbial diversity of sub-visible particles in a submerged anaerobic membrane bioreactor (SAnMBR): Implications for membrane fouling. WATER RESEARCH 2019; 159:20-29. [PMID: 31078091 DOI: 10.1016/j.watres.2019.04.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Sub-visible particles, an often-overlooked fine particle (0.45-10 μm) with a size between sludge solids and soluble microbial products (SMP), have recently been identified as a critical foulant in anaerobic membrane bioreactors (AnMBRs), and our recent new insights into the size-fractionation and composition of sub-visible particles in AnMBRs have enabled fouling to be understood in more depth. Here, we investigated the microbial diversity of the sub-visible particles in three size fractions (i.e., 5-10, 1-5, and 0.45-1 μm) from bulk and cake solutions in a lab-scale AnMBR, and their fouling potential was further explored based on their filtration behavior and biofilm formation. Results show that with decreasing particle size, a significant shift in microbial communities was observed for the sub-visible particles in both bulk and cake solutions; (a) with notable decreases in filamentous microbes in the order SJA-15, GCA004, and Anaerolineales of phylum Chloroflexi, and, (b) with substantial increases in sulfate-reducing bacteria (i.e., the family Syntrophobacteraceae, genus DCE29 of family Thermodesulfovibrionaceae, Desulfovibrio, and Geobacter). More importantly, the filamentous microbes associated with micro-particles (5-10 μm) led to higher cake fouling resistances while free living cells in the form of colloidal particles (0.45-1 μm) induced severer pore blocking. Moreover, the micro-particles had an enhanced capacity to favor biofilm formation (OD595 = 1.0-2.5, categorized as highly positive), thus potentially aggravating biofouling. This work advances our knowledge on the effect of particle size on communities and underlying fouling behavior of microbes associated with fine particles in AnMBRs.
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Affiliation(s)
- Zhongbo Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China; Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Institute (NEWRI), Nanyang Technological University, Singapore, 637141, Singapore
| | - Yu Tao
- Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK
| | - Shaoqing Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Yeyuan Xiao
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Institute (NEWRI), Nanyang Technological University, Singapore, 637141, Singapore; Department of Civil and Environmental Engineering, Shantou University, 515063, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - David C Stuckey
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Institute (NEWRI), Nanyang Technological University, Singapore, 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
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Liu H, Zhang B, Yuan H, Cheng Y, Wang S, He Z. Microbial reduction of vanadium (V) in groundwater: Interactions with coexisting common electron acceptors and analysis of microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1362-1369. [PMID: 28916278 DOI: 10.1016/j.envpol.2017.08.111] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/02/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
Vanadium (V) pollution in groundwater has posed serious risks to the environment and public health. Anaerobic microbial reduction can achieve efficient and cost-effective remediation of V(V) pollution, but its interactions with coexisting common electron acceptors such as NO3-, Fe3+, SO42- and CO2 in groundwater remain unknown. In this study, the interactions between V(V) reduction and reduction of common electron acceptors were examined with revealing relevant microbial community and identifying dominant species. The results showed that the presence of NO3- slowed down the removal of V(V) in the early stage of the reaction but eventually led to a similar reduction efficiency (90.0% ± 0.4% in 72-h operation) to that in the reactor without NO3-. The addition of Fe3+, SO42-, or CO2 decreased the efficiency of V(V) reduction. Furthermore, the microbial reduction of these coexisting electron acceptors was also adversely affected by the presence of V(V). The addition of V(V) as well as the extra dose of Fe3+, SO42- and CO2 decreased microbial diversity and evenness, whereas the reactor supplied with NO3- showed the increased diversity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the accumulation of Geobacter, Longilinea, Syntrophobacter, Spirochaeta and Anaerolinea, which might be responsible for the reduction of multiple electron acceptors. The findings of this study have demonstrated the feasibility of anaerobic bioremediation of V(V) and the possible influence of coexisting electron acceptors commonly found in groundwater.
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Affiliation(s)
- Hui Liu
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution, Ministry of Education, Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution, Ministry of Education, Beijing 100083, China.
| | - Heyang Yuan
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Yutong Cheng
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution, Ministry of Education, Beijing 100083, China
| | - Song Wang
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution, Ministry of Education, Beijing 100083, China
| | - Zhen He
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA.
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Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China. Sci Bull (Beijing) 2017; 62:879-887. [PMID: 36659324 DOI: 10.1016/j.scib.2017.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 01/21/2023]
Abstract
Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.
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Characterization of persistent virus-like particles in two acetate-fed methanogenic reactors. PLoS One 2013; 8:e81040. [PMID: 24278372 PMCID: PMC3838374 DOI: 10.1371/journal.pone.0081040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/18/2013] [Indexed: 11/26/2022] Open
Abstract
The objective of this study was to characterize the morphology, size-distribution, concentration and genome size of virus-like particles (VLPs) in two acetate-fed Methanosaeta-dominated reactors to better understand the possible correlation between viruses and archaeal hosts. The study reactors were dominated by a single genus of acetoclastic methanogen, Methanosaeta, which was present at 6 to 13 times higher than the combined bacterial populations consisting of Proteobacteria, Firmicutes, and Bacteroidetes. Epifluorescent microscopy showed VLPs concentration of 7.1 ± 1.5×107 VLPs/ml and 8.4 ± 4.3×107 VLPs/ml in the two laboratory reactors. Observations of no detectable import of VLPs with the reactor feed combined long operational time since the last inocula were introduced suggests that the VLP populations were actively propagating in the reactors. Transmission electron microscopy images showed VLPs with morphology consistent with Siphoviridae in both reactors, and VLPs with morphologies consistent with Myoviridae in one of the reactors. The morphology, size-distribution and genome size of VLPs were distinct between reactors suggesting that unique viral populations inhabited each reactor, though the hosts of these VLPs remain unclear.
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Nakamura K, Tamaki H, Kang MS, Mochimaru H, Lee ST, Nakamura K, Kamagata Y. A Six-well Plate Method: Less Laborious and Effective Method for Cultivation of Obligate Anaerobic Microorganisms. Microbes Environ 2011; 26:301-6. [DOI: 10.1264/jsme2.me11120] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kohei Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Myung Suk Kang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- National Institute of Biological Resources
| | - Hanako Mochimaru
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Sung-Taik Lee
- Department of Biological Sciences, KAIST (Korea Advanced Institute of Science and Technology)
| | - Kazunori Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Toyohira
- Research Faculty of Agriculture, Hokkaido University
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Carbonero F, Oakley BB, Purdy KJ. Improving the isolation of anaerobes on solid media: the example of the fastidious Methanosaeta. J Microbiol Methods 2009; 80:203-5. [PMID: 19969029 DOI: 10.1016/j.mimet.2009.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/13/2009] [Accepted: 11/20/2009] [Indexed: 11/25/2022]
Abstract
Methanosaeta spp. are globally important biogenic methane producers with only three strains described due to isolation difficulties. Here, clonal axenic isolates from estuarine sediments were obtained using alternative gelling and reducing agents. It is suggested that more systematic approaches with various combinations of media components will help to cultivate difficult-to-isolate anaerobes.
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Affiliation(s)
- Franck Carbonero
- University of Warwick, Department of Biological Sciences, Coventry, CV4 7AL, UK
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Narayanan N, Krishnakumar B, Anupama VN, Manilal VB. Methanosaeta sp., the major archaeal endosymbiont of Metopus es. Res Microbiol 2009; 160:600-7. [PMID: 19695326 DOI: 10.1016/j.resmic.2009.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 07/17/2009] [Accepted: 07/24/2009] [Indexed: 10/20/2022]
Abstract
Epifluorescence microscopy and whole cell in situ hybridization analysis revealed the presence of Methanosaeta sp. as endosymbionts in Metopus es. Direct microscopic observation under epifluorescent microscope showed the presence of long slender rods with an average length of 3.4 microm. The number of methanogenic rods varied from 792 +/- 12 in a single M. es cell with a biovolume of 3.4 x 10(5) microm(3). At the exponential growth stage, a single symbiotic methanogen in M. es produced about 1 fmol methane/h leading to a methane production rate of 0.85 pmol/ciliate/h. The presence of endosymbiotic methanogens in the domain archaea and Methanosaeta sp. was confirmed by FISH with ARCH 915 and MX 825 oligonucleotide probes specific to domain archaea and Methanosaeta respectively. The homogenized cells of M. es also showed bright fluorescing rods with MX 825 hybridization. The culture obtained on inoculation of the released endosymbiotic organisms on Methanosaeta-specific medium lent support to the growth of long slender rods having the same range of mean length (3.6 microm) as that of the endosymbiotic methanogens observed. Both intra- and extracellular production of acetate was detected in M. es culture.
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Affiliation(s)
- Nimi Narayanan
- Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Thiruvananthapuram, 695019 Kerala, India.
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