1
|
Ren Z, Ye S, Li H, Huang X, Chen L, Cao S, Chen T. Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2023; 86:2756-2769. [PMID: 37542537 DOI: 10.1007/s00248-023-02280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.
Collapse
Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 Beijing East Road, Nanjing, 210008, China.
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China.
| | - Shudan Ye
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Hongxuan Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Xilei Huang
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Luyao Chen
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, 768 Jiayuguan W Road, Lanzhou, 730020, China.
| |
Collapse
|
2
|
Yang W, Cai C, Wang R, Dai X. Insights into the impact of quaternary ammonium disinfectant on sewage sludge anaerobic digestion: Dose-response, performance variation, and potential mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130341. [PMID: 36403443 DOI: 10.1016/j.jhazmat.2022.130341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/03/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Wide commercial applications of antimicrobial quaternary ammonium compounds (QACs) inevitably lead to the release into wastewater and enrichment in sewage sludge. This study evaluated the impacts of levels and structures of QACs on sewage sludge properties, microbial community, and methane production during anaerobic digestion. Methane production was stimulated or not affected at low QACs concentrations, but significantly inhibited at high QACs concentrations. Compared with benzyl and alkyltrimethyl QACs, dialkyl QACs showed least toxicity on digestion performance. Meanwhile, microbial community analysis indicated that shifts in bacterial communities mainly depended on QACs doses, but the archaeal communities were affected by both QACs doses and types. The dominant methanogenic pathway shifted from acetotrophic/methylotrophic methanogens to mixotrophic methanogens by low levels of benzyl and alkyltrimethyl QACs but not dialkyl QACs, and further to hydrogenotrophic methanogens at high QACs concentration. Mechanism exploration revealed that the presence of QACs promoted sludge solubilization by the integrated effects of cell lysis, electric neutralization, and hydrophobicity improvement, but inhibited methanogenesis due to the accumulation of volatile fatty acids and susceptibility of methanogens to QACs. These findings provided a reference for potential impacts of different QACs on sludge biological treatment, which had implications for the use and selection of QACs disinfectants.
Collapse
Affiliation(s)
- Wan Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Chen Cai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Rui Wang
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| |
Collapse
|
3
|
Chen W, Zhang D, Luo X, Wang J, Xu Q, Lu X, Mao J, Song H, Wu X, Zan F. In-situ sulfite treatment enhanced the production of short-chain fatty acids from waste activated sludge in the side-stream anaerobic fermentation. BIORESOURCE TECHNOLOGY 2023; 370:128521. [PMID: 36565821 DOI: 10.1016/j.biortech.2022.128521] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Sulfite-based technology could enhance methane production from anaerobic sludge digestion. However, its potential for in-situ direct sludge treatment without anaerobic sludge addition in the side-stream remains unclear. This study investigated the feasibility of using in-situ sulfite treating sludge for short-chain fatty acids (SCFAs) production via anaerobic fermentation of waste activated sludge (WAS) as a side-stream treatment. In-situ sulfite direct sludge treatment enhanced SCFAs and acetic acid production by 2.03 and 4.89 times at 500 mg S/L compared to the control. With in-situ sulfite treatment, WAS hydrolysis and acidification were enhanced while methanogenesis was spontaneously hindered. The in-situ sulfite treatment inactivated pathogens and improved the sludge dewatering properties. The relative abundances of SCFAs-production microbial were stimulated, facilitating the sludge bioconversion. The produced SCFAs from in-situ sulfite side-stream treatment could be applied as an "internal carbon source" to enhance biological nutrient removal to improve economic and environmental value from sludge treatment.
Collapse
Affiliation(s)
- Wei Chen
- School of Urban Construction, Department of Water and Wastewater Engineering and Hubei Experimental Teaching Demonstration Center, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Dandan Zhang
- School of Urban Construction, Department of Water and Wastewater Engineering and Hubei Experimental Teaching Demonstration Center, Wuhan University of Science and Technology, Wuhan 430065, China; School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Luo
- Hubei Provincial Engineering Research Center for Comprehensive Water Environment Treatment in the Yangtze River Basin, Changjiang Institute of Survey, Planning, Design and Research Co., Ltd, Wuhan, China
| | - Jiale Wang
- School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Xu
- Hubei Provincial Engineering Research Center for Comprehensive Water Environment Treatment in the Yangtze River Basin, Changjiang Institute of Survey, Planning, Design and Research Co., Ltd, Wuhan, China
| | - Xiejuan Lu
- School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Mao
- School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjiao Song
- School of Urban Construction, Department of Water and Wastewater Engineering and Hubei Experimental Teaching Demonstration Center, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xiaohui Wu
- School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Low-Carbon Water Environment Technology Center (HUST-SUKE), and Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
4
|
Chaudhry R, Antony B, Batra P, Prakash O. Editorial on the first webinar of the Anaerobic Forum of India. Anaerobe 2022; 78:102650. [PMID: 36273718 DOI: 10.1016/j.anaerobe.2022.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/13/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
| | - Beena Antony
- Department of Microbiology, Father Muller Medical College, Manglore, India
| | - Priyam Batra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Om Prakash
- National Centre for Cell Science, Pune, India
| |
Collapse
|
5
|
The Role of Thermokarst Lake Expansion in Altering the Microbial Community and Methane Cycling in Beiluhe Basin on Tibetan Plateau. Microorganisms 2022; 10:microorganisms10081620. [PMID: 36014037 PMCID: PMC9412574 DOI: 10.3390/microorganisms10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
One of the most significant environmental changes across the Tibetan Plateau (TP) is the rapid lake expansion. The expansion of thermokarst lakes affects the global biogeochemical cycles and local climate regulation by rising levels, expanding area, and increasing water volumes. Meanwhile, microbial activity contributes greatly to the biogeochemical cycle of carbon in the thermokarst lakes, including organic matter decomposition, soil formation, and mineralization. However, the impact of lake expansion on distribution patterns of microbial communities and methane cycling, especially those of water and sediment under ice, remain unknown. This hinders our ability to assess the true impact of lake expansion on ecosystem services and our ability to accurately investigate greenhouse gas emissions and consumption in thermokarst lakes. Here, we explored the patterns of microorganisms and methane cycling by investigating sediment and water samples at an oriented direction of expansion occurred from four points under ice of a mature-developed thermokarst lake on TP. In addition, the methane concentration of each water layer was examined. Microbial diversity and network complexity were different in our shallow points (MS, SH) and deep points (CE, SH). There are differences of microbial community composition among four points, resulting in the decreased relative abundances of dominant phyla, such as Firmicutes in sediment, Proteobacteria in water, Thermoplasmatota in sediment and water, and increased relative abundance of Actinobacteriota with MS and SH points. Microbial community composition involved in methane cycling also shifted, such as increases in USCγ, Methylomonas, and Methylobacter, with higher relative abundance consistent with low dissolved methane concentration in MS and SH points. There was a strong correlation between changes in microbiota characteristics and changes in water and sediment environmental factors. Together, these results show that lake expansion has an important impact on microbial diversity and methane cycling.
Collapse
|
6
|
Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
Collapse
Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| |
Collapse
|
7
|
Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. DIVERSITY 2021. [DOI: 10.3390/d13070328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.
Collapse
|
8
|
Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
Collapse
|
9
|
Pal S, Biswas R, Misra A, Sar A, Banerjee S, Mukherjee P, Dam B. Poorly known microbial taxa dominate the microbiome of hypersaline Sambhar Lake salterns in India. Extremophiles 2020; 24:875-885. [PMID: 32955600 DOI: 10.1007/s00792-020-01201-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/07/2020] [Indexed: 01/21/2023]
Abstract
Inland athalassohaline solar salterns provide unique opportunity to study microbial successions along salinity gradients that resemble transition in natural hypersaline lakes. We analyzed for the first time 16S rRNA gene amplicon sequences of bacteria (V1-V2) and archaea (V4-V5) in saltern brines of India's largest inland hypersaline Sambhar Lake. Brines of the salterns (S1-S4) are alkaline (pH 9.5-10.5) with salinities of 130, 170, 280 and 350 gL-1 respectively. 16S rRNA gene copy-number of archaea outnumbered that of bacteria in all salterns. Their diversity also increased along S1 through S4, while that of bacteria decreased. Brines of S3 and S4 were dominated by specialized extreme halophilic bacterial (Halanaerobiales, Rhodothermaceae) and archaeal (Halobacteriales, Haloferacales) members with recognized salt-in strategy for osmoadaptation. Microbial assemblages positively correlated to saltern pH, total salinity, and ionic composition. Archaea in S1 and S2 were unprecedentedly represented by poorly known as-yet uncultivated groups, Woesearchaeota (90.35-93.51%) and Nanohaloarchaeota that belong to the newly proposed nano-sized superphylum DPANN. In fact, these taxa were identified in archaeal datasets of other athalassohaline salterns after re-analysis using latest RDP database. Thus, microbial compositions in hypersaline lakes are complex and need revisit particularly for their archaeal diversity to understand their hitherto unknown ecological function in extreme environments.
Collapse
Affiliation(s)
- Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Raju Biswas
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Arijit Misra
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Sohini Banerjee
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.,Present address: Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Puja Mukherjee
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.
| |
Collapse
|
10
|
Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E. Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne. Microorganisms 2020; 8:E1394. [PMID: 32932830 PMCID: PMC7565072 DOI: 10.3390/microorganisms8091394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023] Open
Abstract
The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.
Collapse
Affiliation(s)
- Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Anna Schnürer
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Johanna Björkmalm
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Karin Willquist
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Emma Kreuger
- Division of Biotechnology, Department of Chemistry, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| |
Collapse
|
11
|
Malavin S, Shmakova L, Claverie JM, Rivkina E. Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses. Biodivers Data J 2020; 8:e51586. [PMID: 32733138 PMCID: PMC7367895 DOI: 10.3897/bdj.8.e51586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
Background Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to 1000 metres depth. Due to constant subzero temperatures, permafrost represents a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several protist strains and two giant protist viruses isolated from permafrost cores have been already described. New information In this paper, we describe a collection of 35 amoeboid protist strains isolated from the samples of Holocene and Pleistocene permanently frozen sediments. These samples are stored at −18°C in the Soil Cryology Lab, Pushchino, Russia and may be used for further studies and isolation attempts. The collection strains are maintained in liquid media and may be available upon request. The paper also presents a dataset which consists of a table describing the samples and their properties (termed "Sampling events") and a table describing the isolated strains (termed "Occurrences"). The dataset is publicly available through the GBIF portal.
Collapse
Affiliation(s)
- Stas Malavin
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
| | - Lyubov Shmakova
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
| | - Jean-Michel Claverie
- Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Marseille, France Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479) Marseille France
| | - Elizaveta Rivkina
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
| |
Collapse
|
12
|
Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
|
13
|
In 't Zandt MH, Liebner S, Welte CU. Roles of Thermokarst Lakes in a Warming World. Trends Microbiol 2020; 28:769-779. [PMID: 32362540 DOI: 10.1016/j.tim.2020.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/10/2020] [Accepted: 04/01/2020] [Indexed: 11/27/2022]
Abstract
Permafrost covers a quarter of the northern hemisphere land surface and contains twice the amount of carbon that is currently present in the atmosphere. Future climate change is expected to reduce its near-surface cover by over 90% by the end of the 21st century, leading to thermokarst lake formation. Thermokarst lakes are point sources of carbon dioxide and methane which release long-term carbon stocks into the atmosphere, thereby initiating a positive climate feedback potentially contributing up to a 0.39°C rise of surface air temperatures by 2300. This review describes the potential role of thermokarst lakes in a warming world and the microbial mechanisms that underlie their contributions to the global greenhouse gas budget.
Collapse
Affiliation(s)
- Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands; Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, the Netherlands
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section 3.7 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; University of Potsdam, Institute of Biochemistry and Biology, 14469 Potsdam, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands; Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
| |
Collapse
|
14
|
Kallistova AY, Savvichev AS, Rusanov II, Pimenov NV. Thermokarst Lakes, Ecosystems with Intense Microbial Processes of the Methane Cycle. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
15
|
Varliero G, Bienhold C, Schmid F, Boetius A, Molari M. Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front. Front Microbiol 2019; 10:665. [PMID: 31024475 PMCID: PMC6465420 DOI: 10.3389/fmicb.2019.00665] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/18/2019] [Indexed: 11/16/2022] Open
Abstract
Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10°–17°E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats.
Collapse
Affiliation(s)
- Gilda Varliero
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Florian Schmid
- Helmholtz Centre for Ocean Research Kiel, GEOMAR, Kiel, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | |
Collapse
|
16
|
Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front Microbiol 2019; 10:347. [PMID: 30930856 PMCID: PMC6428765 DOI: 10.3389/fmicb.2019.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.
Collapse
Affiliation(s)
- Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eleanna Grammatopoulou
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom
| | - Michelle Pombrol
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Xiaoxiong Xu
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Clifton C Nunnally
- Louisiana Universities Marine Consortium (LUMCON), Chauvin, LA, United States
| | - Jeffrey C Drazen
- Department of Oceanography, University of Hawai'i at Ma-noa, Honolulu, HI, United States
| | - Daniel J Mayor
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom.,National Oceanography Centre, University of Southampton Waterfront Campus European Way, Southampton, United Kingdom
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
17
|
Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, Degenhardt J, Engelen B, Daniel R, Wemheuer B. Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean. ARCHAEA (VANCOUVER, B.C.) 2019; 2019:3717239. [PMID: 31015799 PMCID: PMC6421829 DOI: 10.1155/2019/3717239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/04/2018] [Accepted: 01/08/2019] [Indexed: 01/08/2023]
Abstract
Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.
Collapse
Affiliation(s)
- Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Julius Degenhardt
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| |
Collapse
|
18
|
Dynamics of microbial communities and CO 2 and CH 4 fluxes in the tundra ecosystems of the changing Arctic. J Microbiol 2019; 57:325-336. [PMID: 30656588 DOI: 10.1007/s12275-019-8661-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
Collapse
|
19
|
Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett 2019; 366:5281434. [PMID: 30629179 PMCID: PMC6349945 DOI: 10.1093/femsle/fnz008] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
Collapse
Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jun-Hoe Lee
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, Bristol BS8 1TQ, UK
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| |
Collapse
|
20
|
Luo J, Zhang Q, Wu L, Feng Q, Fang F, Xue Z, Li C, Cao J. Improving anaerobic fermentation of waste activated sludge using iron activated persulfate treatment. BIORESOURCE TECHNOLOGY 2018; 268:68-76. [PMID: 30075331 DOI: 10.1016/j.biortech.2018.06.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/20/2018] [Accepted: 06/23/2018] [Indexed: 05/16/2023]
Abstract
This study reported a novel and efficient approach to improve the anaerobic fermentation performance of waste activated sludge (WAS) by the indigenous iron activated persulfate (PS/Fe) treatment. Firstly, the production of short-chain fatty acids (SCFAs), especially acetic acid, was remarkably enhanced within shorter fermentation time. Mechanism investigations demonstrated that the PS/Fe treatment could simultaneously accelerate and enhance the hydrolysis and acidification process while inhibit the methanogenesis during WAS fermentation. The activities of key enzymes and the abundances of anaerobic microorganisms responsible for SCFAs production were stimulated in the presence of PS/Fe which would promote the biological processes. Secondly, the PS/Fe treatment improved the quality of fermentation residue by reducing the toxic organic compounds in the residue and enhancing the dewaterability of fermented sludge, which was beneficial to the final disposal of WAS with added economical and environmental values.
Collapse
Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qin Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Lijuan Wu
- Jiangsu Provincial Academy of Environmental Science, Nanjing 210098, China
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Zhaoxia Xue
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Chao Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| |
Collapse
|
21
|
Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE. Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources. Front Microbiol 2018; 9:1192. [PMID: 29930542 PMCID: PMC6000721 DOI: 10.3389/fmicb.2018.01192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/16/2018] [Indexed: 12/04/2022] Open
Abstract
Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.
Collapse
Affiliation(s)
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kevin P Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| |
Collapse
|
22
|
Mickol RL, Laird SK, Kral TA. Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars. Microorganisms 2018; 6:microorganisms6020034. [PMID: 29690617 PMCID: PMC6027200 DOI: 10.3390/microorganisms6020034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/25/2023] Open
Abstract
Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.
Collapse
Affiliation(s)
- Rebecca L Mickol
- Arkansas Center for Space and Planetary Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
- American Society for Engineering Education, Washington, DC 20036, USA.
| | - Sarah K Laird
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Timothy A Kral
- Arkansas Center for Space and Planetary Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| |
Collapse
|
23
|
Gonzalez-Martinez A, Sihvonen M, Muñoz-Palazon B, Rodriguez-Sanchez A, Mikola A, Vahala R. Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi. Sci Rep 2018; 8:2208. [PMID: 29396546 PMCID: PMC5797233 DOI: 10.1038/s41598-018-20633-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/21/2018] [Indexed: 01/06/2023] Open
Abstract
Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.
Collapse
Affiliation(s)
- Alejandro Gonzalez-Martinez
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland.
| | - Maija Sihvonen
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
| | | | - Anna Mikola
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Riku Vahala
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| |
Collapse
|
24
|
Yan Y, Ma M, Liu X, Ma W, Li Y. Vertical distribution of archaeal communities associated with anaerobic degradation of pentabromodiphenyl ether (BDE-99) in river-based groundwater recharge with reclaimed water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5154-5163. [PMID: 28871397 DOI: 10.1007/s11356-017-0034-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
When groundwater is recharged with reclaimed water, the presence of trace amounts of biorefractory pentabromodiphenyl ether (PBDE, specifically BDE-99) might cause potential groundwater pollution. A laboratory-scale column was designed to investigate the distribution of the community of archaea in this scenario and the associated anaerobic degradation of BDE-99. The concentration of BDE-99 decreased significantly as soil depth increased, and fluorescence in situ hybridization (FISH) analysis suggested that archaea exerted significant effects on the biodegradation of PBDE. Through 454 pyrosequencing of 16s rRNA genes, we found that the distribution and structure of the archaeal community associated with anaerobic degradation of BDE-99 in the river-based aquifer media changed significantly between different soil depths. The primary debrominated metabolites varied with changes in the vertically distributed archaeal community. The archaea in the surface layer were dominated by Methanomethylovorans, and the middle layer was mainly composed of Nitrososphaera. Nitrosopumilus and Nitrososphaera were equally abundant in the bottom layer. In addition, Methanomethylovorans abundance depended on the depth of soil, and the relative abundance of Nitrosopumilus increased with increasing depth, which was associated with the oxidation-reduction potential and the content of intermediate metabolites. We propose that Nitrososphaera and Nitrosopumilus might be the key archaeal taxa mediating the biodegradation of BDE-99.
Collapse
Affiliation(s)
- Yulin Yan
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Mengsi Ma
- Graduate School of International Relationship, International University of Japan, Minamiuonuma, 9497248, Japan
| | - Xiang Liu
- School of Environmental Engineering, Tsinghua University, Beijing, 100084, China
| | - Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Yangyao Li
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
25
|
Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, Grigoriev MN, Knoblauch C, Mangelsdorf K, Wagner D, Liebner S. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep 2018; 8:1291. [PMID: 29358665 PMCID: PMC5778128 DOI: 10.1038/s41598-018-19505-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022] Open
Abstract
Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.
Collapse
Affiliation(s)
- Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany.
| | - Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Pier P Overduin
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Periglacial Research, 14473, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Maria Winterfeld
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Geochemistry, 27570, Bremerhaven, Germany
| | - Ruud Rijkers
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | | | | | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| |
Collapse
|
26
|
Zhang B, Yue L, Zhou L, Qi L, Li J, Dong X. Conserved TRAM Domain Functions as an Archaeal Cold Shock Protein via RNA Chaperone Activity. Front Microbiol 2017; 8:1597. [PMID: 28878753 PMCID: PMC5572242 DOI: 10.3389/fmicb.2017.01597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Cold shock proteins (Csps) enable organisms to acclimate to and survive in cold environments and the bacterial CspA family exerts the cold protection via its RNA chaperone activity. However, most Archaea do not contain orthologs to the bacterial csp. TRAM, a conserved domain among RNA modification proteins ubiquitously distributed in organisms, occurs as an individual protein in most archaeal phyla and has a structural similarity to Csp proteins, yet its biological functions remain unknown. Through physiological and biochemical studies on four TRAM proteins from a cold adaptive archaeon Methanolobus psychrophilus R15, this work demonstrated that TRAM is an archaeal Csp and exhibits RNA chaperone activity. Three TRAM encoding genes (Mpsy_0643, Mpsy_3043, and Mpsy_3066) exhibited remarkable cold-shock induced transcription and were preferentially translated at lower temperature (18°C), while the fourth (Mpsy_2002) was constitutively expressed. They were all able to complement the cspABGE mutant of Escherichia coli BX04 that does not grow in cold temperatures and showed transcriptional antitermination. TRAM3066 (gene product of Mpsy_3066) and TRAM2002 (gene product of Mpsy_2002) displayed sequence-non-specific RNA but not DNA binding activity, and TRAM3066 assisted RNases in degradation of structured RNA, thus validating the RNA chaperone activity of TRAMs. Given the chaperone activity, TRAM is predicted to function beyond a Csp.
Collapse
Affiliation(s)
- Bo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Liguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| |
Collapse
|
27
|
Elster J, Margesin R, Wagner D, Häggblom M. Editorial: Polar and Alpine Microbiology—Earth's cryobiosphere. FEMS Microbiol Ecol 2016; 93:fiw221. [DOI: 10.1093/femsec/fiw221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/12/2022] Open
|