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Lejal E, Chiquet J, Aubert J, Robin S, Estrada-Peña A, Rue O, Midoux C, Mariadassou M, Bailly X, Cougoul A, Gasqui P, Cosson JF, Chalvet-Monfray K, Vayssier-Taussat M, Pollet T. Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions. MICROBIOME 2021; 9:153. [PMID: 34217365 PMCID: PMC8254910 DOI: 10.1186/s40168-021-01051-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/17/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions. METHODS Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community. RESULTS Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus. CONCLUSIONS We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.
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Affiliation(s)
- E Lejal
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - J Chiquet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - J Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - S Robin
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - A Estrada-Peña
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - O Rue
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - C Midoux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, PROSE, Université Paris-Saclay, Antony, France
| | - M Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - X Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - A Cougoul
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - P Gasqui
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - J F Cosson
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - K Chalvet-Monfray
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | | | - T Pollet
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, Montpellier, France.
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102
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Reddy B, Dubey SK. Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26990-27005. [PMID: 33501578 DOI: 10.1007/s11356-021-12342-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.
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Affiliation(s)
- Bhaskar Reddy
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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103
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Mioduchowska M, Nitkiewicz B, Roszkowska M, Kačarević U, Madanecki P, Pinceel T, Namiotko T, Gołdyn B, Kaczmarek Ł. Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades? Genome 2021; 64:951-958. [PMID: 34015229 DOI: 10.1139/gen-2020-0036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.
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Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.,Department of Marine Plankton Research, Institute of Oceanography, University of Gdansk, Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland; Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Bartosz Nitkiewicz
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, M. Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.,Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Uroš Kačarević
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, J. Hallera 107, 80-416 Gdansk, Poland
| | - Tom Pinceel
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium.,Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Tadeusz Namiotko
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Bartłomiej Gołdyn
- Department of General Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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104
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Wang X, Wu H, Wang X, Wang H, Zhao K, Ma B, Lu Z. Network-directed isolation of the cooperator Pseudomonas aeruginosa ZM03 enhanced the dibutyl phthalate degradation capacity of Arthrobacter nicotianae ZM05 under pH stress. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124667. [PMID: 33279322 DOI: 10.1016/j.jhazmat.2020.124667] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/10/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Dibutyl phthalate (DBP), widely used as plasticizer, is a typical soil contaminant. A new isolate, Arthrobacter nicotianae ZM05, is efficient at degrading DBP but lacks stress resistance to adverse environments. In this study, to isolate effective cooperators of strain ZM05 under pH stress and explore the effects of DBP on the bacterial community structure and interaction between bacteria, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacteria ZM05. 16S rRNA gene sequencing analysis showed that DBP contamination decreased microbial community diversity and weakened potential interactions between microorganisms, evidenced by fewer links, lower average degree, and lower average clustering coefficients in the cooccurrence network. Furthermore, the subnetworks showed that DBP shifted the interactions between strain ZM05 and other microbes. Based on the prediction of the network, the nondegrading bacterium Pseudomonas aeruginosa ZM03 was isolated and proven through coculture experiments to have a positive interaction with strain ZM05 during DBP degradation under pH stress. Strain ZM03 could utilize downstream acidic metabolites to alleviate acid inhibition and accelerate degradation. This study provides solid evidence that bacterial communities adjust their interactions to adapt to DBP stress and provides new insight into the prediction of microbes that are cooperative with degrading bacteria.
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Affiliation(s)
- Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
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105
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Xu R, Fan F, Lin Q, Yuan S, Meng F. Overlooked Ecological Roles of Influent Wastewater Microflora in Improving Biological Phosphorus Removal in an Anoxic/Aerobic MBR Process. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6270-6280. [PMID: 33830745 DOI: 10.1021/acs.est.0c07891] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The ecological roles of influent microflora in activated sludge communities have not been well investigated. Herein, parallel lab-scale anoxic/aerobic (A/O) membrane bioreactors (MBRs), which were fed with raw (MBR-C) and sterilized (MBR-T) municipal wastewater, were operated. The MBRs showed comparable nitrogen removal but superior phosphorus removal in MBR-C than MBR-T over the long-term operation. The MBR-C sludge community had higher diversity and deterministic assembly than the MBR-T sludge community as revealed by 16S rRNA gene sequencing and null model analysis. Moreover, the MBR-C sludge community had higher abundance of polyphosphate accumulating organisms (PAOs) and hydrolytic/fermentative bacteria (HFB) but lower abundance of glycogen-accumulating organisms (GAOs), in comparison with MBR-T sludge. Intriguingly, the results of both the net growth rate and Sloan's neutral model demonstrated that HFB in the sludge community were generally slow-growing or nongrowing and their consistent presence in activated sludge was primarily attributed to the HFB immigration from influent microflora. Positive correlations between PAOs and HFB and potential competitions between HFB and GAOs were observed, as revealed by the putative species-species associations in the ecological networks. Taken together, this work deciphers the positive ecological roles of influent microflora, particularly HFB, in system functioning and highlights the necessity of incorporating influent microbiota for the design and modeling of A/O MBR plants.
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Affiliation(s)
- Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, P. R. China
| | - Fuqiang Fan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, P. R. China
| | - Qining Lin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, P. R. China
| | - Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, P. R. China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, P. R. China
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106
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Fei X, Lina W, Jiayang C, Meng F, Guodong W, Yaping Y, Langjun C. Variations of microbial community in Aconitum carmichaeli Debx. rhizosphere soilin a short-term continuous cropping system. J Microbiol 2021; 59:481-490. [PMID: 33779961 DOI: 10.1007/s12275-021-0515-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Aconitum carmichaeli Debx. (Ranunculaceae) is a potential source of an important herbal drug named "Fuzi", which is derived from the lateral root of the plant. Increased therapeutic usage resulted in the great demand for artificial cultivation of A. carmichaeli, however, the obstacles caused by continuous cropping is a serious problem. Continuous cropping has shown to affect the soil biological and non-biological factors. The current study attempted to discover the variations of microbial communities and soil properties in short-term continuous cropping of A. carmichaeli. An experimental procedure with A. carmichaeli planted two years continuously was established. The variation of the soil microbial community, disease incidence, soil properties, and the correlation between soil microbe and disease incidence were investigated. The disease incidence increased during the continuous cropping of A. carmichaeli. The PCoA and LefSe results indicated that fungal communities in rhizosphere soil were altered during the short-term continuous croppingand the bacterial community was disturbed by the cultivation of A. carmichaeli, however, in the following two years of continuous cropping period, the soil bacterial community has not changed obviously. Proportions of some fungal and bacterial genera were varied significantly (p < 0.05), and some genera of microflora showed a significant correlation with adisease incidence of A. carmichaeli. Microorganisms contributing to community composition discrepancy were also elucidated. Continuous cropping of A. carmichaeli disturbed the rhizosphere soil microbial community and altered the soil chemical parameters and soil pH. These variations in soil may be related to the occurrence of plant diseases. The current study will not only provide theoretical and experimental evidence for the A. carmichaeli continuous cropping obstacles but will also contribute to A. carmichaeli agricultural production and soil improvement.
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Affiliation(s)
- Xia Fei
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'An, 710021, China
| | - Wang Lina
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Chen Jiayang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Fu Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Wang Guodong
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Yan Yaping
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Cui Langjun
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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107
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Nyirabuhoro P, Gao X, Ndayishimiye JC, Xiao P, Mo Y, Ganjidoust H, Yang J. Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir. FEMS Microbiol Ecol 2021; 97:6184044. [PMID: 33755730 DOI: 10.1093/femsec/fiab036] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
Investigation of bacterial community dynamics across different time scales is important for understanding how environmental conditions drive community change over time. Bacterioplankton from the surface waters of a subtropical urban reservoir in southeast China were analyzed through high-frequency sampling over 13 months to compare patterns and ecological processes between short (0‒8 weeks), medium (9‒24 weeks) and long (25‒53 weeks) time intervals. We classified the bacterial community into different subcommunities: abundant taxa (AT); conditionally rare taxa (CRT); rare taxa (RT). CRT contributed > 65% of the alpha-diversity, and temporal change of beta-diversities was more pronounced for AT and CRT than RT. The bacterial community exhibited a directional change in the short- and medium-time intervals and a convergent dynamic during the long-time interval due to a seasonal cycle. Cyanobacteria exhibited a strong succession pattern than other phyla. CRT accounted for > 76% of the network nodes in three stations. The bacteria-environment relationship and deterministic processes were stronger for large sample size at station G (n = 116) than small sample size at stations C (n = 12) and L (n = 22). These findings suggest that a high-frequency sampling approach can provide a better understanding on the time scales at which bacterioplankton can change fast between being abundant or rare, thus providing the facts about environmental factors driving microbial community dynamics. Patterns and processes in alpha- and beta-diversities and community assembly of bacterioplankton differ among different time intervals (short-, medium- and long-time intervals) and different subcommunities (abundant, conditionally rare and rare taxa) in a subtropical urban reservoir, demonstrating the importance of temporal scale and high-frequency sampling in microbial community ecology.
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Affiliation(s)
- Pascaline Nyirabuhoro
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaofei Gao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jean Claude Ndayishimiye
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hossein Ganjidoust
- Faculty of Civil and Environmental Engineering, Environmental Engineering Division, Tarbiat Modares University, P.O. Box 14115-397, Tehran, Iran
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China
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108
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Capo E, Ninnes S, Domaizon I, Bertilsson S, Bigler C, Wang XR, Bindler R, Rydberg J. Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene. Microorganisms 2021; 9:microorganisms9020355. [PMID: 33670228 PMCID: PMC7916980 DOI: 10.3390/microorganisms9020355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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Affiliation(s)
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
- Correspondence:
| | - Sofia Ninnes
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Isabelle Domaizon
- UMR CARRTEL, INRAE, Université Savoie Mont Blanc, 74200 Thonon les Bains, France;
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, SLU, 75007 Uppsala, Sweden;
| | - Christian Bigler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Richard Bindler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Johan Rydberg
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
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109
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Loftus M, Hassouneh SAD, Yooseph S. Bacterial associations in the healthy human gut microbiome across populations. Sci Rep 2021; 11:2828. [PMID: 33531651 PMCID: PMC7854710 DOI: 10.1038/s41598-021-82449-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.
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Affiliation(s)
- Mark Loftus
- grid.170430.10000 0001 2159 2859Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32787 USA
| | - Sayf Al-Deen Hassouneh
- grid.170430.10000 0001 2159 2859Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32787 USA
| | - Shibu Yooseph
- grid.170430.10000 0001 2159 2859Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816-2993 USA
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110
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Zhang H, Zong R, He H, Liu K, Yan M, Miao Y, Ma B, Huang X. Biogeographic distribution patterns of algal community in different urban lakes in China: Insights into the dynamics and co-existence. J Environ Sci (China) 2021; 100:216-227. [PMID: 33279034 DOI: 10.1016/j.jes.2020.07.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 06/12/2023]
Abstract
Urban lake ecosystems are significant for social development, but currently we know little about the geographical distribution of algal community in urban lakes at a large-scale. In this study, we investigated the algal community structure in different areas of urban lakes in China and evaluated the influence of water quality parameters and geographical location on the algal community. The results showed that obvious differences in water quality and algal communities were observed among urban lakes in different geographical areas. Chlorophyta was the dominant phylum, followed by cyanobacteria in all areas. The network analysis indicated that algal community composition in urban lakes of the western and southern area showed more variations than the eastern and northern areas, respectively. Redundancy analysis and structural equation model revealed that nutrients and pH were dominant environmental factors that affected the algal community, and they showed higher influence than that of iron, manganese and COD Mn concentration. Importantly, algal community and density exhibited longitude and latitude relationship. In general, these results provided an ecological insight into large-scale geographical distributions of algal community in urban lakes, thereby having potential applications for management of the lakes.
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Affiliation(s)
- Haihan Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Rongrong Zong
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Huiyan He
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kaiwen Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Miaomiao Yan
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yutian Miao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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111
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Li D, Ni H, Jiao S, Lu Y, Zhou J, Sun B, Liang Y. Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies. MICROBIOME 2021; 9:20. [PMID: 33482926 PMCID: PMC7825242 DOI: 10.1186/s40168-020-00978-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/07/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. RESULTS The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. CONCLUSIONS These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.
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Affiliation(s)
- Dong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Environmental and Safety Engineering, Changzhou University, Changzhou, 213164, China
| | - Haowei Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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112
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Park JG, Lee B, Heo TY, Cheon AI, Jun HB. Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes. BIORESOURCE TECHNOLOGY 2021; 319:124205. [PMID: 33045546 DOI: 10.1016/j.biortech.2020.124205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 05/25/2023]
Abstract
Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO2--N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.
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Affiliation(s)
- Jun-Gyu Park
- Department of Environmental Engineering, Chungbuk National University, Cheongju 28644, Republic of Korea; Department of Environmental Engineering, Montana Technological University, Butte, MT 59701, USA.
| | - Beom Lee
- Department of Environmental Engineering, Chungbuk National University, Cheongju 28644, Republic of Korea; Nature Engineering Co., LTD., 1 Chungdae-ro, Cheongju 28644, Republic of Korea.
| | - Tae-Young Heo
- Department of Information Statistics, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - A-In Cheon
- Department of Environmental Engineering, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Hang-Bae Jun
- Department of Environmental Engineering, Chungbuk National University, Cheongju 28644, Republic of Korea.
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113
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Ya T, Du S, Li Z, Liu S, Zhu M, Liu X, Jing Z, Hai R, Wang X. Successional Dynamics of Molecular Ecological Network of Anammox Microbial Communities under Elevated Salinity. WATER RESEARCH 2021; 188:116540. [PMID: 33126006 DOI: 10.1016/j.watres.2020.116540] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Response of microbial interactions to environmental perturbations has been a central issue in wastewater treatment system. However, the interactions among anammox microbial community under salt perturbation is still unclear. Here, we used random matrix theory (RMT)-based network analysis to investigate the dynamics of networks under elevated salinity in an anammox system. Results showed that high salinity (20 and 30 g/L NaCl) inhibited anammox performance. Salinity led to closer and more complex networks for the overall network and subnetwork of Planctomycetes and Proteobacteria, especially under low salinity (5 g/L NaCl), which could serve as a strategy to survive under salt perturbation. Planctomycetes, most dominant phylum and playing crucial roles in anammox, possessed higher proportion of competitive relationships (64.3%) under 30 g/L NaCl. OTU 109 (closely related to Ignavibacterium), the only network hub detected in the anammox system, also had larger amount of competitive relationships (27.3%) than the control (0%) under 30 g/L NaCl. Similar result was found for the most abundant keystone bacteria Candidatus Kuenenia. These increasing competitions at different taxa level could be responsible for the deterioration of nitrogen removal. Besides, all the network topological features tended to reach the values of the original network, which showed the network of microbial community could gradually adapt to the elevated salinity. Microbial network analysis adds a different dimension for our understanding of the response in microbial community to elevated salinity.
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Affiliation(s)
- Tao Ya
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuai Du
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Guo Dian Fu Tong Science and Technology Development Co., Ltd., Beijing 100070
| | - Zhenyang Li
- Airport New City in Xixian New Area Management Commission of Shaanxi Province, Xi'an, 712034, China
| | - Shidi Liu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Minghan Zhu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaojing Liu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zibo Jing
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Reti Hai
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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114
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Yang J, Jiang H, Sun X, Huang J, Han M, Wang B. Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity. FEMS Microbiol Ecol 2020; 97:5989694. [PMID: 33206972 DOI: 10.1093/femsec/fiaa234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China.,Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
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115
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Qu Z, Forster D, Bruni EP, Frantal D, Kammerlander B, Nachbaur L, Pitsch G, Posch T, Pröschold T, Teubner K, Sonntag B, Stoeck T. Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility. Mol Ecol 2020; 30:1053-1071. [PMID: 33306859 DOI: 10.1111/mec.15776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022]
Abstract
Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co-occurrence networks constructed from time-series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate-specific subnetworks resembled autecological species-specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co-occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate-stressed ecosystems.
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Affiliation(s)
- Zhishuai Qu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Estelle P Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Katrin Teubner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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116
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Li N, Li X, Shi ZY, Fan XY, Zhou ZW. Response of high-, mid- and low-abundant taxa and potential pathogens to eight disinfection methods and their interactions in domestic hot water system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141440. [PMID: 32829270 DOI: 10.1016/j.scitotenv.2020.141440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Eight disinfection methods were applied to control biofilm contamination in domestic hot water system. The inactivation efficiency, responses of high- (≥1%), mid- (0.1% ~ 1%) and low-abundant taxa (≤0.1%) to disinfection, and interactions within and across three sub-communities were investigated. Ultraviolet was the most effective disinfection method for total bacteria and Escherichia coli, and chlorine dioxide had the highest inactivation efficiency on heterotrophic bacteria, while silver ions exhibited poor performance on all of them. At the phylum level, the responses of microorganisms to eight disinfection methods were different, but Proteobacteria and Firmicutes dominated in most samples. Eight disinfection methods had a greater impact on the proportion of high- and mid-abundant taxa than that of low-abundant taxa, and led to dissimilar transformations of genera among high-, mid- and low-abundant taxa in each sample. High-, mid- and low-abundant taxa of different samples showed similar structures and were roughly clustered into three Groups. Moreover, high-abundant taxa had more complex internal interactions than mid- and low-abundant taxa, and mainly presented co-occurrence patterns. The associations between high- and low-abundant taxa were close, and some low-abundant genera were identified as hub bacteria, such as Paracoccus, Thioalkalispira and Flavitalea. Furthermore, a total of 23 potential pathogens were detected in this study, and they mainly showed positive interactions, with Mycobacteria and Streptococcus as keystone genera. These results highlight the dissimilar responses of high-, mid- and low-abundant taxa to disinfection, and the critical role of some low-abundant genera in the microbial network, as well as the co-occurrence patterns among potential pathogens.
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Affiliation(s)
- Na Li
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Xing Li
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Zhi-Yuan Shi
- Shanghai Investigation, Design & Research Institute Co., Ltd, Shanghai 200335, PR China
| | - Xiao-Yan Fan
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, PR China.
| | - Zhi-Wei Zhou
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, PR China
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117
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Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [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: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
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118
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Wu G, Ge L, Zhao N, Liu F, Shi Z, Zheng N, Zhou D, Jiang X, Halverson L, Xie B. Environment dependent microbial co-occurrences across a cyanobacterial bloom in a freshwater lake. Environ Microbiol 2020; 23:327-339. [PMID: 33185973 DOI: 10.1111/1462-2920.15315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/28/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022]
Abstract
Microbial taxon-taxon co-occurrences may directly or indirectly reflect the potential relationships between the members within a microbial community. However, to what extent and the specificity by which these co-occurrences are influenced by environmental factors remains unclear. In this report, we evaluated how the dynamics of microbial taxon-taxon co-occurrence is associated with the changes of environmental factors in Nan Lake at Wuhan city, China with a Modified Liquid Association method. We were able to detect more than 1000 taxon-taxon co-occurrences highly correlated with one or more environmental factors across a phytoplankton bloom using 16S rRNA gene amplicon community profiles. These co-occurrences, referred to as environment dependent co-occurrences (ED_co-occurrences), delineate a unique network in which a taxon-taxon pair exhibits specific, and potentially dynamic correlations with an environmental parameter, while the individual relative abundance of each may not. Microcystis involved ED_co-occurrences are in important topological positions in the network, suggesting relationships between the bloom dominant species and other taxa could play a role in the interplay of microbial community and environment across various bloom stages. Our results may broaden our understanding of the response of a microbial community to the environment, particularly at the level of microbe-microbe associations.
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Affiliation(s)
- Gang Wu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Leixin Ge
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Na Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Fei Liu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Zunji Shi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Ningning Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Dan Zhou
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China.,School of Biological Sciences, Guizhou Normal College, Guiyang, Guizhou, 550018, China
| | - Xingpeng Jiang
- School of Computer, Central China Normal University, Wuhan, 430079, China
| | - Larry Halverson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
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Szabó A, Korponai K, Somogyi B, Vajna B, Vörös L, Horváth Z, Boros E, Szabó-Tugyi N, Márialigeti K, Felföldi T. Grazing pressure-induced shift in planktonic bacterial communities with the dominance of acIII-A1 actinobacterial lineage in soda pans. Sci Rep 2020; 10:19871. [PMID: 33199773 PMCID: PMC7669872 DOI: 10.1038/s41598-020-76822-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Astatic soda pans of the Pannonian Steppe are unique environments with respect to their multiple extreme physical and chemical characteristics (high daily water temperature fluctuation, high turbidity, alkaline pH, salinity, polyhumic organic carbon concentration, hypertrophic state and special ionic composition). However, little is known about the seasonal dynamics of the bacterial communities inhabiting these lakes and the role of environmental factors that have the main impact on their structure. Therefore, two soda pans were sampled monthly between April 2013 and July 2014 to reveal changes in the planktonic community. By late spring in both years, a sudden shift in the community structure was observed, the previous algae-associated bacterial communities had collapsed, resulting the highest ratio of Actinobacteria within the bacterioplankton (89%, with the dominance of acIII-A1 lineage) ever reported in the literature. Before these peaks, an extremely high abundance (> 10,000 individuum l-1) of microcrustaceans (Moina brachiata and Arctodiaptomus spinosus) was observed. OTU-based statistical approaches showed that in addition to algal blooms and water-level fluctuations, zooplankton densities had the strongest effect on the composition of bacterial communities. In these extreme environments, this implies a surprisingly strong, community-shaping top-down role of microcrustacean grazers.
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Affiliation(s)
- Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary.
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Boglárka Somogyi
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Balázs Vajna
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Lajos Vörös
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Zsófia Horváth
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Emil Boros
- Centre for Ecological Research, Danube Research Institute, Karolina út 29, Budapest, 1113, Hungary
| | - Nóra Szabó-Tugyi
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
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120
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Kang J, Park JS, Jung SW, Kim HJ, Joo HM, Kang D, Seo H, Kim S, Jang MC, Lee KW, Jin Oh S, Lee S, Lee TK. Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms. Mol Ecol 2020; 30:207-221. [PMID: 33113287 PMCID: PMC7839783 DOI: 10.1111/mec.15714] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/24/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023]
Abstract
Characterizing ecological relationships between viruses, bacteria and phytoplankton in the ocean is critical to understanding the ecosystem; however, these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Specific bacterial species showed complex synergistic and antagonistic relationships with the A. sanguinea bloom. The endoparasitic dinoflagellate Amoebophrya sp. 1 controlled the bloom dynamics and correlated with HAB decline. Among nucleocytoplasmic large DNA viruses (NCLDVs), two Pandoraviruses and six Phycodnaviruses were strongly and positively correlated with the HABs. Operational taxonomic units of microbial communities and environmental factors associated with A. sanguinea were visualized by network analysis: A. sanguinea-Amoebophrya sp. 1 (r = .59, time lag: 2 days) and A. sanguinea-Ectocarpus siliculosus virus 1 in Phycodnaviridae (0.50, 4 days) relationships showed close associations. The relationship between A. sanguinea and dissolved inorganic phosphorus relationship also showed a very close correlation (0.74, 0 day). Microbial communities and the environment changed dynamically during the A. sanguinea bloom, and the rapid turnover of microorganisms responded to ecological interactions. A. sanguinea bloom dramatically changes the environments by exuding dissolved carbohydrates via autotrophic processes, followed by changes in microbial communities involving host-specific viruses, bacteria and parasitoids. Thus, the microbial communities in HAB are composed of various organisms that interact in a complex manner.
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Affiliation(s)
- Junsu Kang
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje, Korea.,Department of Oceanography, Pukyong National University, Busan, Korea
| | - Joon Sang Park
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje, Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje, Korea
| | - Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje, Korea
| | - Hyoung Min Joo
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, Korea
| | - Donhyug Kang
- Maritime Security Research Center, Korea Institute of Ocean Science & Technology, Busan, Korea
| | - Hyojeong Seo
- Department of Oceanography, Pukyong National University, Busan, Korea
| | - Sunju Kim
- Department of Oceanography, Pukyong National University, Busan, Korea
| | - Min-Chul Jang
- Ballast Water Research Center, Korea Institute of Ocean Science & Technology, Geoje, Korea
| | - Kyun-Woo Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Korea
| | - Seok Jin Oh
- Department of Oceanography, Pukyong National University, Busan, Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Taek-Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje, Korea
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121
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Allen GR, Schwartz FW, Cole DR, Lanno RP, Prabhu A, Eleish A. Algal blooms in a freshwater reservoir – A network community detection analysis of potential forcing parameters. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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122
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Zhang L, Fang W, Li X, Lu W, Li J. Strong linkages between dissolved organic matter and the aquatic bacterial community in an urban river. WATER RESEARCH 2020; 184:116089. [PMID: 32693265 DOI: 10.1016/j.watres.2020.116089] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Aquatic bacterial communities play an important role in biogeochemical cycling in river ecosystems; however, knowledge of the linkages between bacterial communities and dissolved organic matter (DOM) in urban rivers is limited. Here, 16S rRNA amplicon sequencing and parallel factor (PARAFAC) modeling of excitation-emission fluorescence spectroscopy were used to analyze the compositions, co-occurrence patterns, and interactions with chromophoric DOM (CDOM) of bacterial communities in urban river water samples influenced by different human activities. The results revealed that two protein-like components accounted for 65.2 ± 9.56% of the total variability in all three fluorescence components, which suggests that CDOM in urban rivers is mainly a microbial source. In addition to pH and DO, CDOM is also an important factor affecting bacterial community structure, and the main classes (Gammaproteobacteria and Clostridia) and genera (Limnohabitans and Alpinimonas) showed strong positive correlations with terrestrial humic-like C1 and tryptophan-like C2, respectively. When autotrophic and heterotrophic bacteria coexist in urban rivers, the production and degradation of CDOM will occur simultaneously. Furthermore, the riverine bacterial co-occurrence network had a nonrandom modular structure, which was mainly driven by classification correlation and bacterial function. The high abundance of genes related to xenobiotic metabolism, carbon metabolism and nitrogen metabolism in the urban river indicated that anthropogenic activity may be the dominant selective force altering the bacterial communities. Overall, our results provide a novel view for the assembly of bacterial communities in urban river ecosystems under the influence of different human activities.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
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123
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Abstract
This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied. While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.
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124
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Zhou J, Lao YM, Song JT, Jin H, Zhu JM, Cai ZH. Temporal heterogeneity of microbial communities and metabolic activities during a natural algal bloom. WATER RESEARCH 2020; 183:116020. [PMID: 32653764 DOI: 10.1016/j.watres.2020.116020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/31/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the interactions between algae and associated microbial communities is critical for understanding the mechanisms that mediate the dynamic of harmful algal blooms (HABs) in marine environment. However, the microbial functional profiles and their biogeochemical potential in HABs process remains elusive, especially during a complete natural HAB cycle. Here, we used pyrosequencing and functional gene array (GeoChip) to investigate microbial community dynamics and metabolic potential during a natural dinoflagellate (Noctiluca scintillans) bloom. The results shown that bacterioplankton exhibited significant temporal heterogeneity over the course of the bloom stages. Microbial succession was co-driven by environmental parameters and biotic interactions. The functional analysis revealed significant variations in microbial metabolism during matter cycling. At bloom onset-stage, metabolic potential associated with iron oxidation and transport was elevated. Carbon fixation and degradation, denitrification, phosphorus acquisition, and sulfur transfer/oxidation were significantly enhanced at the plateau stage. During the decline and terminal stages, oxidative stress, lysis of compounds, and toxin degradation & protease synthesis increased. This work reveal phycosphere microorganisms can enhanced organic C decomposition capacity, altered N assimilation rate and S/P turnover efficiency, and balancing of the Fe budget during HAB process. The ecological linkage analysis has further shown that microbial composition and functional potential were significantly linked to algal blooms occurrence. It suggest that structural variability and functional plasticity of microbial communities influence HAB trajectory.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Yong-Min Lao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jun-Ting Song
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Hui Jin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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125
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Kang X, Cui Y, Shen T, Yan M, Tu W, Shoaib M, Xiang Q, Zhao K, Gu Y, Chen Q, Li S, Liang Y, Ma M, Zou L, Yu X. Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110816. [PMID: 32521370 DOI: 10.1016/j.ecoenv.2020.110816] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 05/28/2023]
Abstract
Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.
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Affiliation(s)
- Xia Kang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China; Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Yongliang Cui
- Sichuan Provincial Academy of Natural Resource and Sciences, Chengdu, 610015, China
| | - Tian Shen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiguo Tu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Shoaib
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfu Gu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuangcheng Li
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yueyang Liang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China.
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126
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Babalola OO, Fadiji AE, Enagbonma BJ, Alori ET, Ayilara MS, Ayangbenro AS. The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies. Front Microbiol 2020; 11:548037. [PMID: 33013781 PMCID: PMC7499240 DOI: 10.3389/fmicb.2020.548037] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
The diversity of plant-associated microbes is enormous and complex. These microbiomes are structured and form complex interconnected microbial networks that are important in plant health and ecosystem functioning. Understanding the composition of the microbiome and their core function is important in unraveling their networking strategies and their potential influence on plant performance. The network is altered by the host plant species, which in turn influence the microbial interaction dynamics and co-evolution. We discuss the plant microbiome and the complex interplay among microbes and between their host plants. We provide an overview of how plant performance is influenced by the microbiome diversity and function.
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Affiliation(s)
- Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayomide E Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ben J Enagbonma
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Elizabeth T Alori
- Department of Crop and Soil Sciences, Landmark University, Omu-Aran, Nigeria
| | - Modupe S Ayilara
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayansina S Ayangbenro
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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127
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Shao Q, Lin Z, Zhou C, Yan X. Bacterioplankton assembly and interspecies interactions follow trajectories of Gymnodinium-diatom bloom. MARINE ENVIRONMENTAL RESEARCH 2020; 160:105010. [PMID: 32907730 DOI: 10.1016/j.marenvres.2020.105010] [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: 12/02/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
The underlying mechanisms of bacterioplankton community assembly and interspecies interactions during harmful algal blooms remain largely unclear. Using 16S rRNA gene amplicon sequencing, we analyzed the bacterioplankton communities over the continuous course of saxitoxin-producing Gymnodinium catenatum blooms and two diatom (i.e., Skeletonema costatum and Chaetoceros curvisetus) blooms in an anthropogenically controlled and eutrophic bay, East China Sea. The succession of bacterioplankton communities correlated with changes in the dynamics of algal species. Deterministic versus stochastic bacterioplankton community assemblage processes were quantified, demonstrating that stochastic processes increased when algal blooms happened. The occurrence of algal blooms caused weaker bacterioplankton interspecies interactions and higher degrees of cooperative activities, changed keystone taxa and diminished the stability of bacterial communities. These findings consequently have important implications for our understanding of bacterioplankton community ecology during algal blooms.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Zhongzhou Lin
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Chengxu Zhou
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
| | - Xiaojun Yan
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
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128
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Wan W, Zhang Y, Cheng G, Li X, Qin Y, He D. Dredging mitigates cyanobacterial bloom in eutrophic Lake Nanhu: Shifts in associations between the bacterioplankton community and sediment biogeochemistry. ENVIRONMENTAL RESEARCH 2020; 188:109799. [PMID: 32798942 DOI: 10.1016/j.envres.2020.109799] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Cyanobacterial blooms are a worldwide environmental problem, which is partly attributed to their access to excessive nitrogen (N) and phosphorus (P). Preventing the blooms by reducing N and P from internal inputs is viewed as a challenge. To evaluate the effects of dredging on cyanobacterial abundances and bacterioplankton communities, water and sediment samples were collected from eutrophic Lake Nanhu (Wuhan, China) before dredging (2017) and after dredging (2018). After dredging, significant decreases were observed for sediment nutrients (e.g., C, N, and P sources); C-, N-, P-, and S-cycling-related enzyme activity; N- and P-cycling-related gene abundance; microbial abundance; and dramatic changes were observed in the composition of the sediment microbial community. The release rates of nutrient including nitrogen, phosphorus, and organic matter decreased after dredging, and sediment biogeochemistry was closely correlated to nutrient release rates. Additionally, our observations and analyses indicated that the abundance and diversity of the bacterioplankton community decreased significantly, the composition and interaction of the bacterioplankton community dramatically changed, and the bacterioplankton community function (e.g., N, P-cycling-related enzymes and proteins) down regulated after dredging. Water and sediment physicochemical factors explained 72.28% variation in bacterioplankton community composition, and these physicochemical factors were significantly correlated with diversity, composition, and function of bacterioplankton community. Our findings emphasized that cyanobacterial blooms in freshwater ecosystems were closely correlated with noncyanobacterial bacterioplankton that were largely conserved at the phylum level, with Proteobacteria, Actinobacteria, and Bacteroidetes as the main taxa. To our knowledge, this is the first report clarifying the mechanism of cyanobacterial blooms mitigation by dredging, via changing the association between the bacterioplankton community and sediment biogeochemistry. Our findings are of significance and indicate that dredging is effective for mitigating cyanobacterial blooms.
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Affiliation(s)
- Wenjie Wan
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yunan Zhang
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China
| | - Guojun Cheng
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China
| | - Xiaohua Li
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China
| | - Yin Qin
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China
| | - Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan, 430070, PR China.
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129
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A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities. ISME JOURNAL 2020; 14:3011-3023. [PMID: 32770118 DOI: 10.1038/s41396-020-0733-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/09/2020] [Accepted: 07/28/2020] [Indexed: 11/08/2022]
Abstract
Lakes play a pivotal role in ecological and biogeochemical processes and have been described as "sentinels" of environmental change. Assessing "lake health" across large geographic scales is critical to predict the stability of their ecosystem services and their vulnerability to anthropogenic disturbances. The LakePulse research network is tasked with the assessment of lake health across gradients of land use on a continental scale. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet large-scale responses to anthropogenic activity remain elusive. Here, we assess the ecological impact of land use on bacterial communities from over 200 lakes covering more than 660,000 km2 across Eastern Canada. In addition to community variation between ecozones, land use across Eastern Canada also appeared to alter diversity, community composition, and network structure. Specifically, increasing anthropogenic impact within the watershed lowered diversity. Likewise, community composition was significantly correlated with agriculture and urban development within a watershed. Interaction networks showed decreasing complexity and fewer keystone taxa in impacted lakes. Moreover, we identified potential indicator taxa of high or low lake water quality. Together, these findings point to detectable bacterial community changes of largely unknown consequences induced by human activity within lake watersheds.
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130
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Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger. Front Microbiol 2020; 11:1665. [PMID: 32793154 PMCID: PMC7393233 DOI: 10.3389/fmicb.2020.01665] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.
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Affiliation(s)
- Yao Ning
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jinzhe Qi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Michael T Dobbins
- Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Xin Liang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jingxuan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shiyu Chen
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangshun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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131
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Silva MOD, Pernthaler J. Biomass addition alters community assembly in ultrafiltration membrane biofilms. Sci Rep 2020; 10:11552. [PMID: 32665605 PMCID: PMC7360762 DOI: 10.1038/s41598-020-68460-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
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Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
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132
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Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment. mSphere 2020; 5:5/4/e00354-20. [PMID: 32611696 PMCID: PMC7333569 DOI: 10.1128/msphere.00354-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.
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133
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Zhao M, Ma YT, He SY, Mou X, Wu L. Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China. FEMS Microbiol Ecol 2020; 96:5863183. [DOI: 10.1093/femsec/fiaa064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 06/25/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.
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Affiliation(s)
- Man Zhao
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Yan-tian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Shi-yao He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, OH 44242, USA
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
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134
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Tian H, Xu X, Qu J, Li H, Hu Y, Huang L, He W, Li B. Biodegradation of phenolic compounds in high saline wastewater by biofilms adhering on aerated membranes. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122463. [PMID: 32193113 DOI: 10.1016/j.jhazmat.2020.122463] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
High saline phenolic wastewater is a typical toxic and refractory industrial wastewater. A single membrane-aerated biofilm reactor (MABR) was used to treat wastewater containing phenol, p-nitrophenol and hydroquinone under increasing phenolic loading and salinity conditions. More than 95 % of phenolic compounds were removed, and a removal efficiency of 8.9 g/m2 d for total phenolic (TP) contents was achieved under conditions with 32 g/L of salt and 763 mg/L of influent TP contents. The microbial diversity, structure and function of a biofilm exposed to different conditions were investigated by high-throughput 16S rRNA gene sequencing and metagenomics. Salinity and specific TP loading substantially affected the bacterial community. Gammaproteobacteria, Actinobacteria and Betaproteobacteria contributed more to initial phenolic compound degradation than other classes, with Pseudomonas and Rhodococcus as the main contributing genera. The key phenolic-degrading genes of different metabolic pathways were explored, and their relative abundance was strengthened with increasing phenolic loading and salinity. The diverse cooperation and competition patterns of these microorganisms further promoted the high removal efficiency of multiple phenolic contaminants in the biofilms. These results demonstrate the feasibility of MABR for degrading multiple phenolic compounds in high saline wastewater.
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Affiliation(s)
- Hailong Tian
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Xingjian Xu
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, PR China
| | - Jianhang Qu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China.
| | - Haifeng Li
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Yanzhuo Hu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Liang Huang
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Wentian He
- Shanghai Majorbio Bio-pharm Technology Co.,Ltd, Shanghai 201203, PR China
| | - Baoan Li
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; College of Environmental Science and Engineering, Nankai University, Tianjin 300072, PR China.
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135
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Lemonnier C, Perennou M, Eveillard D, Fernandez-Guerra A, Leynaert A, Marié L, Morrison HG, Memery L, Paillard C, Maignien L. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. FRONTIERS IN MARINE SCIENCE 2020. [DOI: 10.3389/fmars.2020.00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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136
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Juottonen H, Fontaine L, Wurzbacher C, Drakare S, Peura S, Eiler A. Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly. Environ Microbiol 2020; 22:3158-3171. [PMID: 32372550 DOI: 10.1111/1462-2920.15058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/22/2020] [Accepted: 05/02/2020] [Indexed: 01/04/2023]
Abstract
Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.
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Affiliation(s)
- Heli Juottonen
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, 40014, Finland
| | - Laurent Fontaine
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, Oslo, 0371, Norway
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, Göteborg, 405 30, Sweden.,Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, Garching, 85748, Germany
| | - Stina Drakare
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SLU, Box 7050, Uppsala, 750 07, Sweden
| | - Sari Peura
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 75007, Sweden
| | - Alexander Eiler
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, Oslo, 0371, Norway.,eDNA solutions AB, Björkåsgatan 16, Mölndal, 43131, Sweden
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137
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Wu H, Xia J, Qin X, Wu H, Zhang S, Zhao Y, Rensing C, Lin W. Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover. Front Microbiol 2020; 11:1142. [PMID: 32528459 PMCID: PMC7266878 DOI: 10.3389/fmicb.2020.01142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
Abstract
Replanting disease caused by negative plant-soil feedback in continuous monoculture of Radix pseudostellariae is a critical factor restricting the development of this common and popular Chinese medicine, although wild R. pseudostellariae plants were shown to grow well without occurrence of disease in the same site for multiple years. Therefore, we aimed to identify the changes in microbial community composition in the rhizosphere soil of wild R. pseudostellariae thus providing a potential method for controlling soil-borne diseases. We analyzed differences in soil physicochemical properties, changes in soil microbial community structure, and root exudates of wild R. pseudostellariae under different biotopes. And then, simple sequence repeats amplification was used to isolate and collect significantly different formae speciales of Fusarium oxysporum. Finally, we analyzed the pathogenicity testing and influence of root exudates on the growth of F. oxysporum. We found that the different biotopes of R. pseudostellariae had significant effects on the soil microbial diversity. The soil fungal and bacterial abundances were significantly higher and the abundance of F. oxysporum was significantly lower under the rhizosphere environment of wild R. pseudostellariae than under consecutive monoculture. The relative abundances of most genera were Penicillium, Aspergillus, Fusarium, Nitrobacter, Nitrospira, Streptomyces, Actinoplanes, and Pseudomonas. Venn diagram and LEfSe analyses indicated numerously specific microbiome across all the samples, and the numbers of specific fungi were higher than the shared ones in the four biotopes. Eight types of phenolic acids were identified across all the rhizosphere soils. Mixed phenolic acids and most of the examined single phenolic acids had negative effects on the growth of isolated pathogenic F. oxysporum strains and promoted the growth of non-pathogenic strains. Similarly, correlation analysis suggested that most of the identified phenolic acids were positively associated with beneficial Pseudomonas, Nitrobacter, Nitrospira, Streptomyces, and Bacillus. This study suggested that wild R. pseudostellariae was able to resist or tolerate disease by increasing soil microbial diversity, and reducing the accumulation of soil-borne pathogens.
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Affiliation(s)
- Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinshen Xia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiming Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengkai Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
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138
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Yin Z, Sun K, Li A, Sun D, Li Z, Xiao G, Feng J. Changes in the gut microbiota during Asian particolored bat ( Vespertilio sinensis) development. PeerJ 2020; 8:e9003. [PMID: 32435532 PMCID: PMC7227643 DOI: 10.7717/peerj.9003] [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: 08/14/2019] [Accepted: 03/26/2020] [Indexed: 12/26/2022] Open
Abstract
Background The gut microbiota is closely linked to host development, diet and health and is influenced by both the host and the environment. Although many studies have focused on the dynamics of the gut microbiota during development in captive animals, few studies have focused on the dynamics of the gut microbiota during development in wild animals, especially for the order Chiroptera. Methods In this study, we characterized the gut microbiota of the wild Asian particolored bat (Vespertilio sinensis) from 1 day to 6 weeks after birth. We explored the changes in their gut microbial community compositions, examined possible influencing factors, and predicted the feeding transition period. Results The gut microbiota changed during the development of V. sinensis. The alpha diversity of the bats' gut microbiota gradually increased but did not change significantly from the 1st day to the 4th week after birth; however, the alpha diversity decreased significantly in week 5, then stabilized. The beta diversity differed slightly in weeks 4-6. In week 4, the fecal samples showed the highest diversity in bacterial community composition. Thus, we predicted that the potential feeding transition period for V. sinensis may occur during week 4. Redundancy analysis showed that age and body mass index significantly affected the compositional changes of the gut microbiota in Asian particolored bats. Conclusion The gut microbiota changed during the development of V. sinensis. We suggest that changes in the alpha and beta diversity during week 4 after birth indicate a potential feeding transition, highlighting the importance of diet in the gut microbiota during the development of V. sinensis.
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Affiliation(s)
- Zhongwei Yin
- College of Life Science, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Deyi Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Guohong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
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139
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Quero GM, Celussi M, Relitti F, Kovačević V, Del Negro P, Luna GM. Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait). MICROBIAL ECOLOGY 2020; 79:823-839. [PMID: 31728602 DOI: 10.1007/s00248-019-01451-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.
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Affiliation(s)
- Grazia Marina Quero
- Stazione Zoologica Anton Dohrn, Integrative Marine Ecology Department, Napoli, Italy
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
| | - Federica Relitti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Vedrana Kovačević
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Gian Marco Luna
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
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140
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Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems. Sci Rep 2020; 10:6012. [PMID: 32265458 PMCID: PMC7138807 DOI: 10.1038/s41598-020-62919-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 03/09/2020] [Indexed: 11/25/2022] Open
Abstract
Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, the drivers of microbial community structure remain unexplored in maize cropping systems under complex and variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing and network analysis to identify the major environmental factors driving bacterial community diversity and co-occurrence patterns in 21 maize field soils across China. The results show that mean annual precipitation and soil pH are the major environmental factors that shape soil bacterial communities in maize soils. The similarities of bacterial communities significantly decreased with increasing geographic distance between different sites. The differences in spatial turnover rates across bacterial phyla indicate the distinct dispersal capabilities of bacterial groups, and some abundant phyla exhibited high dispersal capabilities. Aeromicrobium, Friedmanniella, Saccharothrix, Lamia, Rhodococcus, Skermanella, and Pedobacter were identified as keystone taxa. Based on the node-level and network-level topological features, members of the core microbiome were more frequently found in the center of the ecosystem network compared with other taxa. This study highlights the major environmental factors driving bacterial community assembly in agro-ecosystems and the central ecological role of the core microbiome in maintaining the web of complex bacterial interactions.
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141
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Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
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Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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142
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Hu Y, Yao X, Wu Y, Han W, Zhou Y, Tang X, Shao K, Gao G. Contrasting Patterns of the Bacterial Communities in Melting Ponds and Periglacial Rivers of the Zhuxi glacier in the Tibet Plateau. Microorganisms 2020; 8:microorganisms8040509. [PMID: 32252494 PMCID: PMC7232332 DOI: 10.3390/microorganisms8040509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/04/2022] Open
Abstract
Since the early 21st century, global climate change has been inducing rapid glacier retreat at an unprecedented rate. In this context, the melt ponds impart increasing unique footprints on the periglacial rivers due to their hydrodynamic connection. Given that bacterial communities control numerous ecosystem processes in the glacial ecosystem, exploring the fate of bacterial communities from melt ponds to periglacial rivers yields key knowledge of the biodiversity and biogeochemistry of glacial ecosystems. Here, we analyzed the bacterial community structure, diversity, and co-occurrence network to reveal the community organization in the Zhuxi glacier in the Tibet Plateau. The results showed that the bacterial communities in melt ponds were significantly lower in alpha-diversity but were significantly higher in beta-diversity than those in periglacial rivers. The rare sub-communities significantly contributed to the stability of the bacterial communities in both habitats. The co-occurrence network inferred that the mutually beneficial relationships predominated in the two networks. Nevertheless, the lower ratio of positive to negative edges in melt ponds than periglacial rivers implicated fiercer competition in the former habitat. Based on the significantly higher value of degree, betweenness, and modules, as well as shorter average path length in melt ponds, we speculated that their bacterial communities are less resilient than those of periglacial rivers.
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Affiliation(s)
- Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Xin Yao
- School of Environment and Planning, Liaocheng University, Liaocheng 25200, China
| | - Yuanyuan Wu
- Sino-Japan Friendship Center for Environmental Protection, Beijing 100029, China
| | - Wei Han
- Sino-Japan Friendship Center for Environmental Protection, Beijing 100029, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
- Correspondence: ; Tel.: (+86) 25 86882187; Fax: (+86) 25 86882187
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143
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Mioduchowska M, Zając K, Bartoszek K, Madanecki P, Kur J, Zając T. 16S rRNA
gene‐based metagenomic analysis of the gut microbial community associated with the DUI species
Unio crassus
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Katarzyna Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science Division of Statistics and Machine Learning Linköping University Linköping Sweden
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany Faculty of Pharmacy Medical University of Gdańsk Gdańsk Poland
| | | | - Tadeusz Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
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144
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Xu R, Zhang S, Meng F. Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity. WATER RESEARCH 2020; 170:115307. [PMID: 31786395 DOI: 10.1016/j.watres.2019.115307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 05/06/2023]
Abstract
Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.
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Affiliation(s)
- Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Shaoqing Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China.
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145
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Abstract
Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean. Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups. IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.
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146
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Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance. mSystems 2020; 5:5/1/e00357-19. [PMID: 31911462 PMCID: PMC6946792 DOI: 10.1128/msystems.00357-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biotic interactions among members of microbial communities have been conceived to be crucial for community assembly, it remains unclear how changes in environmental conditions affect microbial interaction and consequently system performance. Here, we adopted a random matrix theory-based network analysis to explore microbial interactions in triplicate anaerobic digestion (AD) systems, which is widely applied for organic pollutant treatments. The digesters were operated with incremental organic loading rates (OLRs) from 1.0 g volatile solids (VS)/liter/day to 1.3 g VS/liter/day and then to 1.5 g VS/liter/day, which increased VS removal and methane production proportionally. Higher resource availability led to networks with higher connectivity and shorter harmonic geodesic distance, suggestive of more intense microbial interactions and quicker responses to environmental changes. Strikingly, a number of topological properties of microbial network showed significant (P < 0.05) correlation with AD performance (i.e., methane production, biogas production, and VS removal). When controlling for environmental parameters (e.g., total ammonia, pH, and the VS load), node connectivity, especially that of the methanogenic archaeal network, still correlated with AD performance. Last, we identified the Methanothermus, Methanobacterium, Chlorobium, and Haloarcula taxa and an unclassified Thaumarchaeota taxon as keystone nodes of the network.IMPORTANCE AD is a biological process widely used for effective waste treatment throughout the world. Biotic interactions among microbes are critical to the assembly and functioning of the microbial community, but the response of microbial interactions to environmental changes and their influence on AD performance are still poorly understood. Using well-replicated time series data of 16S rRNA gene amplicons and functional gene arrays, we constructed random matrix theory-based association networks to characterize potential microbial interactions with incremental OLRs. We demonstrated striking linkage between network topological features of methanogenic archaea and AD functioning independent of environmental parameters. As the intricate balance of multiple microbial functional groups is responsible for methane production, our results suggest that microbial interaction may be an important, previously unrecognized mechanism in determining AD performance.
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147
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Kaczmarek Ł, Roszkowska M, Poprawa I, Janelt K, Kmita H, Gawlak M, Fiałkowska E, Mioduchowska M. Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis. Mol Phylogenet Evol 2020; 145:106730. [PMID: 31904510 DOI: 10.1016/j.ympev.2019.106730] [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: 08/10/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/26/2022]
Abstract
In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and morphometric characters of the eggs. The p-distance between two COI haplotypes of Pam. experimentalis sp. nov. was 0.17%. In turn, the ranges of uncorrected genetic p-distances of all Paramacrobiotus species available in GenBank was from 18.27% (for Pam. lachowskae) to 25.26% (for Pam. arduus) with an average distance of 20.67%. We also found that Pam. experimentalis sp. nov. is bisexual. This observation was congruent on three levels: (i) morphological - specimen size dimorphism; (ii) structural (primary sexual characteristics) - females have an unpaired ovary while males have an unpaired testis and (iii) molecular - heterozygous and homozygous strains of the ITS-2 marker. Although symbiotic associations of hosts with bacteria (including endosymbiotic bacteria) are common in nature and these interactions exert various effects on the evolution, biology and reproductive ecology of hosts, there is still very little information on the bacterial community associated with tardigrades. To fill this gap and characterise the bacterial community of Pam. experimentalis sp. nov. populations and microbiome of its microhabitat, high throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed. The obtained 16S rRNA gene sequences ranged from 92,665 to 131,163. In total, 135 operational taxonomic units (OTUs) were identified across the rarefied dataset. Overall, both Pam. experimentalis sp. nov. populations were dominated by OTUs ascribed to the phylum Proteobacteria (89-92%) and Firmicutes (6-7%). In the case of samples from tardigrades' laboratory habitat, the most abundant bacterial phylum was Proteobacteria (51-90%) and Bacteroides (9-48%). In all compared microbiome profiles, only 16 of 137 OTUs were shared. We found also significant differences in beta diversity between the partly species-specific microbiome of Pam. experimentalis sp. nov. and its culturing environment. Two OTUs belonging to a putative bacterial endosymbiont were identified - Rickettsiales and Polynucleobacter. We also demonstrated that each bacterial community was rich in genes involved in membrane transport, amino acid metabolism, and carbohydrate metabolism.
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Affiliation(s)
- Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Izabela Poprawa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland.
| | - Kamil Janelt
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Hanna Kmita
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Magdalena Gawlak
- The Institute of Plant Protection-National Research Institute, Węgorka 20, 60-318 Poznań, Poland.
| | - Edyta Fiałkowska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Monika Mioduchowska
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
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148
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Zhou L, Zhou Y, Yao X, Cai J, Liu X, Tang X, Zhang Y, Jang KS, Jeppesen E. Decreasing diversity of rare bacterial subcommunities relates to dissolved organic matter along permafrost thawing gradients. ENVIRONMENT INTERNATIONAL 2020; 134:105330. [PMID: 31759274 DOI: 10.1016/j.envint.2019.105330] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 05/28/2023]
Abstract
Dissolved organic matter (DOM) released from permafrost thaw greatly influences the biogeochemical cycles of, among others, downstream carbon, nitrogen and phosphorus cycles; yet, knowledge of the linkages between bacterial communities with permafrost DOM heterogeneity is limited. Here, we aim at unravelling the responses of bacterial diversities and metabolic profiles to DOM quantity and composition across permafrost thawing gradients by coupling an extensive field investigation with bio-incubation experiments. Richness, evenness and dissimilarities of the whole and rare communities decreased from thermokarst pits to headstreams and to downstream rivers. The assemblages of the abundant subcommunities were mainly determined by ecological drift-driven stochastic processes. Both the optical and the molecular composition of DOM were significantly related to the changes of the whole (rare) bacterial communities (Mantel's correlation > 0.5, p < 0.01). Diversity indices of the whole and rare communities decreased with decreasing relative abundance of tannins, condensed aromatics and more aromatic and oxidized lignins as well as with decreased dissolved organic carbon and intensities of all fluorescence components. Laboratory DOM bio-incubation experiments further confirmed microbial consumption of more aromatic and oxidized compounds as well as decreasing metabolic diversities in terms of microbial degradation and production along permafrost thawing gradients. Our findings suggest that changes in the sources of permafrost-derived DOM induced by global warming can have different influences on the diversity and metabolism of bacterial communities and thus on permafrost carbon climate feedbacks along permafrost thawing gradients.
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Affiliation(s)
- Lei Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Yao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Cai
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Shanghai Municipal Engineering Design Institute (Group) CO., LTD, Shanghai 200092, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlin Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Erik Jeppesen
- Department of Bioscience and Arctic Research Centre, Aarhus University, DK-8600 Silkeborg, Denmark; Sino-Danish Centre for Education and Research, Beijing 100190, China; Limnology Laboratory and EKOSAM, Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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149
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Garcia J, Kao‐Kniffin J. Can dynamic network modelling be used to identify adaptive microbiomes? Funct Ecol 2019. [DOI: 10.1111/1365-2435.13491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Joshua Garcia
- School of Integrative Plant Science Cornell University Ithaca NY USA
| | - Jenny Kao‐Kniffin
- School of Integrative Plant Science Cornell University Ithaca NY USA
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150
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Zhang H, Hou F, Xie W, Wang K, Zhou X, Zhang D, Zhu X. Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process. Environ Microbiol 2019; 22:1707-1719. [PMID: 31599072 DOI: 10.1111/1462-2920.14820] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 02/01/2023]
Abstract
Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co-occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α-diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. β-Diversity of the RS was the highest among three subcommunities, and the variation of β-diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co-occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum. Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Fanrong Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Weijuan Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiaoyan Zhou
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
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