1
|
Jin H, Li L, Lu W, Zhang Z, Xing Y, Wu D. Identification of the regulatory roles of water qualities on the spatio-temporal dynamics of microbiota communities in the water and fish guts in the Heilongjiang River. Front Microbiol 2024; 15:1435360. [PMID: 39234540 PMCID: PMC11372393 DOI: 10.3389/fmicb.2024.1435360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
The Heilongjiang River is one of the largest rivers in the cool temperate zone and has an abundant fish source. To date, the microbiota community in water samples and fish guts from the Heilongjiang River is still unclear. In the present study, water samples and fish guts were collected from four locations of the Heilongjiang River during both the dry season and the wet season to analyze the spatio-temporal dynamics of microbiota communities in the water environment and fish guts through 16s ribosome RNA sequencing. The water qualities showed seasonal changes in which the pH value, dissolved oxygen, and total dissolved solids were generally higher during the dry season, and the water temperature was higher during the wet season. RDA indicated that higher pH values, dissolved oxygen, and total dissolved solids promoted the formation of microbiota communities in the water samples of the dry season, while higher water temperature positively regulated the formation of microbiota communities in the water samples of the wet season. LEFSe identified five biomarkers with the most abundant difference at the genus level, of which TM7a was upregulated in the water samples of the dry season, and SM1A02, Rheinheimera, Gemmatimonas, and Vogesella were upregulated in the water samples of the wet season. Pearson analysis revealed that higher pH values and dissolved oxygen positively regulated the formation of TM7a and negatively regulated the formation of SM1A02, Rheinheimera, Gemmatimonas, and Vogesella (p < 0.05), while higher water temperature had the opposite regulatory roles in the formation of these biomarkers. The relative abundance of microbiota diversity in fish guts varies greatly between different fish species, even if the fishes were collected from the same water source, indicating that dietary habits and fish species may be key factors, affecting the formation and construction of microbiome community in fish gut. P. glenii, P. lagowskii, G. cynocephalus, and L. waleckii were the main fish resources, which were collected and identified from at least six sample points. RDA indicated that the microbiota in the water environment regulated the formation of microbiota community in the guts of G. cynocephalus and L. waleckii and had limited regulated effects on P. glenii and P. lagowskii. The present study identified the regulatory effects of water qualities on the formation of microbiota communities in the water samples and fish guts, providing valuable evidence for the protection of fish resources in the Heilongjiang River.
Collapse
Affiliation(s)
- Hongyu Jin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Lei Li
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Wanqiao Lu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Zepeng Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Yue Xing
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Di Wu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| |
Collapse
|
2
|
Xie G, Sun C, Gong Y, Luo W, Tang X. Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake. MICROBIAL ECOLOGY 2024; 87:96. [PMID: 39046558 PMCID: PMC11269507 DOI: 10.1007/s00248-024-02410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.
Collapse
Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wenlei Luo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- The Fuxianhu Station of Plateau Deep Lake Field Scientific Observation and Research, Yuxi, 653100, Yunnan, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
3
|
Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
Collapse
Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
4
|
Mäkelä K, Laanto E, Sundberg LR. Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases. Environ Microbiol 2024; 26:e16670. [PMID: 38952172 DOI: 10.1111/1462-2920.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/24/2024] [Indexed: 07/03/2024]
Abstract
The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.
Collapse
Affiliation(s)
- Kati Mäkelä
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| |
Collapse
|
5
|
Mohan R, Pillai SS, Purushothaman A, Thomas LC, Padmakumar KB. Phylogenic diversity of bacteria associated with potentially toxic cyanobacteria Microcystis aeruginosa: a synthesis on its bloom dynamics. Folia Microbiol (Praha) 2024; 69:677-691. [PMID: 37991690 DOI: 10.1007/s12223-023-01108-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The occurrence of toxic bloom-forming cyanobacteria, Microcystis aeruginosa, has been frequently reported worldwide. These colony forming toxic cyanobacteria harbour a wide range of heterotrophic bacterial communities. The present study has attempted to understand the bloom dynamics of M. aeruginosa along with isolating their colony-associated culturable heterotrophic bacteria from two freshwater ponds in south India with a persisting cyanobacterial bloom. The monthly monitoring of these study areas revealed the conducive role of warm, stagnant waters with high nutrients in forming M. aeruginosa bloom. The peak values of temperature, nitrate, and phosphate at station 1 reached up to 30.5 °C, 4.48 mg/L, 1.64 mg/L, and at station 2, 31 °C, 3.45 mg/L, and 0.62 mg/L, respectively. Twenty-eight bacterial isolates belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes were obtained during the study. Among these 28 isolates, Firmicutes was dominant with the M. aeruginosa bloom from both the study areas.
Collapse
Affiliation(s)
- Renju Mohan
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Sreya S Pillai
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Aishwarya Purushothaman
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - Lathika Cicily Thomas
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India
| | - K B Padmakumar
- Department of Marine Biology, Microbiology & Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi-16, Kerala, India.
| |
Collapse
|
6
|
Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
Collapse
Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| |
Collapse
|
7
|
Reignier O, Bormans M, Hervé F, Robert E, Savar V, Tanniou S, Amzil Z, Noël C, Briand E. Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum. HARMFUL ALGAE 2024; 134:102627. [PMID: 38705620 DOI: 10.1016/j.hal.2024.102627] [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: 01/26/2024] [Revised: 03/22/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to climate changes and eutrophication, blooms of predominantly toxic freshwater cyanobacteria are intensifying and are likely to colonize estuaries, thus impacting benthic organisms and shellfish farming representing a major ecological, health and economic risk. In the natural environment, Microcystis form large mucilaginous colonies that influence the development of both cyanobacterial and embedded bacterial communities. However, little is known about the fate of natural colonies of Microcystis by salinity increase. In this study, we monitored the fate of a Microcystis dominated bloom and its microbiome along a French freshwater-marine gradient at different phases of a bloom. We demonstrated changes in the cyanobacterial genotypic composition, in the production of specific metabolites (toxins and compatible solutes) and in the heterotrophic bacteria structure in response to the salinity increase. In particular M. aeruginosa and M. wesenbergii survived salinities up to 20. Based on microcystin gene abundance, the cyanobacteria became more toxic during their estuarine transfer but with no selection of specific microcystin variants. An increase in compatible solutes occurred along the continuum with extensive trehalose and betaine accumulations. Salinity structured most the heterotrophic bacteria community, with an increased in the richness and diversity along the continuum. A core microbiome in the mucilage-associated attached fraction was highly abundant suggesting a strong interaction between Microcystis and its microbiome and a likely protecting role of the mucilage against an osmotic shock. These results underline the need to better determine the interactions between the Microcystis colonies and their microbiome as a likely key to their widespread success and adaptation to various environmental conditions.
Collapse
Affiliation(s)
| | - Myriam Bormans
- UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes F-35042, France
| | - Fabienne Hervé
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Elise Robert
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France
| | | | - Simon Tanniou
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Zouher Amzil
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Cyril Noël
- IFREMER, IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Enora Briand
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France.
| |
Collapse
|
8
|
Lu Z, Cai Q, Lai S, Chen N, Huang L, Liu Y, Lei L, Gan S, Zhang L, Paerl HW, Wang F. Coupling of cylindrospermopsin and pho-harboring Verrucomicrobia supports the formation of Raphidiopsis blooms in low-phosphorus waters. WATER RESEARCH 2024; 250:121010. [PMID: 38142507 DOI: 10.1016/j.watres.2023.121010] [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: 08/18/2023] [Revised: 10/26/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
Cylindrospermopsin (CYN) can induce phytoplankton community to secrete alkaline phosphatase (ALP), which is one of the important strategies for the bloom-forming cyanobacterium Raphidiopsis to thrive in extremely low-phosphorus (P) waters. However, how bacterioplankton community, another major contributor to ALPs in waters, couples to Raphidiopsis through CYN, and the role of this coupling in supporting the dominance of Raphidiopsis in nature remain largely unknown. Here, we conducted microcosm experiments to address this knowledge gap, using a combination of differential filtration-based and metagenomics-based methods to identify the sources of ALPs. We found that, compared with algal-derived ALPs, bacteria-derived ALPs exhibited a more pronounced and sensitive response to CYN. This response to CYN was enhanced under low-P conditions. Interestingly, we found that Verrucomicrobia made the largest contribution to the total abundance of pho genes, which encode ALPs. Having high gene abundance of the CYN-sensing PI3K-AKT signaling pathway, Verrucomicrobia's proportion increased with higher concentrations of CYN under low-P conditions, thereby explaining the observed increase in pho gene abundance. Compared with other cyanobacterial genera, Raphidiopsis had a higher abundance of the pst gene. This suggests that Raphidiopsis exhibited a greater capacity to uptake the inorganic P generated by ALPs secreted by other organisms. Overall, our results reveal the mechanism of CYN-induced ALP secretion and its impact on planktonic P-cycling, and provide valuable insights into the role of CYN in supporting the formation of Raphidiopsis blooms.
Collapse
Affiliation(s)
- Zhe Lu
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China.
| | - Qijia Cai
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Guangzhou, 510655, PR China
| | - Shuyan Lai
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China
| | - Nan Chen
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China
| | - Lincheng Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510650, PR China
| | - Yongxin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510650, PR China
| | - Lamei Lei
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China.
| | - Shuchai Gan
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China
| | - Lulu Zhang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China
| | - Hans W Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel Hill, Morehead City, USA
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China.
| |
Collapse
|
9
|
Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM. Flexible genomic island conservation across freshwater and marine Methylophilaceae. THE ISME JOURNAL 2024; 18:wrad036. [PMID: 38365254 PMCID: PMC10872708 DOI: 10.1093/ismejo/wrad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
Collapse
Affiliation(s)
- Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| |
Collapse
|
10
|
Rodríguez-Gijón A, Hampel JJ, Dharamshi J, Bertilsson S, Garcia SL. Shotgun metagenomes from productive lakes in an urban region of Sweden. Sci Data 2023; 10:810. [PMID: 37978200 PMCID: PMC10656542 DOI: 10.1038/s41597-023-02722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.
Collapse
Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
| | - Justyna J Hampel
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Jennah Dharamshi
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129, Oldenburg, Germany.
| |
Collapse
|
11
|
Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
Collapse
Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
12
|
Srivastava A, Verma D. Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27552-7. [PMID: 37217817 DOI: 10.1007/s11356-023-27552-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.
Collapse
Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
| |
Collapse
|
13
|
Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
Collapse
Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
| |
Collapse
|
14
|
Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China. BMC Microbiol 2023; 23:47. [PMID: 36823577 PMCID: PMC9948317 DOI: 10.1186/s12866-023-02793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.
Collapse
|
15
|
Crevecoeur S, Edge TA, Watson LC, Watson SB, Greer CW, Ciborowski JJH, Diep N, Dove A, Drouillard KG, Frenken T, McKay RM, Zastepa A, Comte J. Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum. Front Microbiol 2023; 14:1073753. [PMID: 36846788 PMCID: PMC9947797 DOI: 10.3389/fmicb.2023.1073753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.
Collapse
Affiliation(s)
- Sophie Crevecoeur
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada,*Correspondence: Sophie Crevecoeur, ✉
| | - Thomas A. Edge
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Linet Cynthia Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Susan B. Watson
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Charles W. Greer
- Energy, Mining and Environment, National Research Council of Canada, Montreal, QC, Canada
| | - Jan J. H. Ciborowski
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada,Department of Biological Sciences University of Calgary, Calgary, AB, Canada
| | - Ngan Diep
- Ontario Ministry of the Environment, Conservation and Parks, Environmental Monitoring and Reporting Branch, Etobicoke, ON, Canada
| | - Alice Dove
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Kenneth G. Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Cluster Nature & Society, HAS University of Applied Sciences, s-Hertogenbosch, Netherlands
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - Arthur Zastepa
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, Quebec City, QC, Canada,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université de Montréal, Montreal, QC, Canada
| |
Collapse
|
16
|
Wang H, Liu X, Wang Y, Zhang S, Zhang G, Han Y, Li M, Liu L. Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers. J Environ Sci (China) 2023; 124:187-197. [PMID: 36182129 DOI: 10.1016/j.jes.2021.10.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/15/2021] [Accepted: 10/11/2021] [Indexed: 06/16/2023]
Abstract
The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH3-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.
Collapse
Affiliation(s)
- Hongjie Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Xingchun Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Yali Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Shengqi Zhang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Guangming Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Yangyang Han
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Mengxiang Li
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Ling Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China.
| |
Collapse
|
17
|
Hanashiro FTT, De Meester L, Vanhamel M, Mukherjee S, Gianuca AT, Verbeek L, van den Berg E, Souffreau C. Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition. MICROBIAL ECOLOGY 2023; 85:400-410. [PMID: 35306576 DOI: 10.1007/s00248-022-01994-x] [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: 08/21/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.
Collapse
Affiliation(s)
- Fabio Toshiro T Hanashiro
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium.
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB), Müggelseedamm 310, 12587, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195, Berlin, Germany
| | - Matthias Vanhamel
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Laboratory of Reproductive Genomics, KU Leuven, ON I Herestraat 49, 3000, Leuven, Belgium
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, 59078-900, Brazil
| | - Laura Verbeek
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Edwin van den Berg
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| |
Collapse
|
18
|
Te SH, Kok JWK, Luo R, You L, Sukarji NH, Goh KC, Sim ZY, Zhang D, He Y, Gin KYH. Coexistence of Synechococcus and Microcystis Blooms in a Tropical Urban Reservoir and Their Links with Microbiomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1613-1624. [PMID: 36653016 PMCID: PMC9894078 DOI: 10.1021/acs.est.2c04943] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria-cyanobacteria interactions contributed significantly to phytoplankton dynamics. However, information on the contribution of bacterial communities to blooms remains scarce. Here, we tracked changes in the bacterial community during the development of a cyanobacterial bloom in an equatorial estuarine reservoir. Two forms of blooms were observed simultaneously corresponding to the lotic and lentic characteristics of the sampling sites where significant spatial variabilities in physicochemical water quality, cyanobacterial biomass, secondary metabolites, and cyanobacterial/bacterial compositions were detected. Microcystis dominated the upstream sites during peak periods and were succeeded by Synechococcus when the bloom subsided. For the main body of the reservoir, a mixed bloom featuring coccoid and filamentous cyanobacteria (Microcystis, Synechococcus, Planktothricoides, Nodosilinea, Raphidiopsis, and Prochlorothrix) was observed. Concentrations of the picocyanobacteria Synechococcus remained high throughout the study, and their positive correlations with cylindrospermopsin and anatoxin-a suggested that they could produce cyanotoxins, which pose more damaging impacts than previously supposed. Succession of different cyanobacteria (Synechococcus and Microcystis) following changes in nutrient composition and ionic strength was demonstrated. The microbiomes associated with blooms were unique to the dominant cyanobacteria. Generic and specialized bloom biomarkers for the Microcystis and downstream mixed blooms were also identified. Microscillaceae, Chthoniobacteraceae, and Roseomonas were the major heterotrophic bacteria associated with Microcystis bloom, whereas Phycisphaeraceae and Methylacidiphilaceae were the most prominent groups for the Synechococcus bloom. Collectively, bacterial community can be greatly deviated by the geological condition, monsoon season, cyanobacterial density, and dominant cyanobacteria.
Collapse
Affiliation(s)
- Shu Harn Te
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Jerome Wai Kit Kok
- Department
of Civil and Environmental Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, 117576 Singapore
| | - Rong Luo
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Luhua You
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Nur Hanisah Sukarji
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Kwan Chien Goh
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Zhi Yang Sim
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Dong Zhang
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
| | - Yiliang He
- School
of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- National
University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, 138602 Singapore
- Department
of Civil and Environmental Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, 117576 Singapore
| |
Collapse
|
19
|
Zhu J, Yang F, Du K, Wei ZL, Wu QF, Chen Y, Li WF, Li Q, Zhou CZ. Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer. ENVIRONMENTAL MICROBIOME 2023; 18:3. [PMID: 36639816 PMCID: PMC9837993 DOI: 10.1186/s40793-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. RESULTS Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. CONCLUSION In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.
Collapse
Affiliation(s)
- Jie Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zi-Lu Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| |
Collapse
|
20
|
Wu D, Zhao J, Su Y, Yang M, Dolfing J, Graham DW, Yang K, Xie B. Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria. WATER RESEARCH 2023; 228:119359. [PMID: 36423548 DOI: 10.1016/j.watres.2022.119359] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/30/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 106 cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.
Collapse
Affiliation(s)
- Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guizhou 550001, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Jue Zhao
- Department of Civil and Environmental Engineering and Research Institute for Sustainable Urban Development, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Mengjie Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Jan Dolfing
- Faculty Energy and Environment, Northumbria University, Newcastle upon Tyne, NE1 8QH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Kai Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| |
Collapse
|
21
|
Zakharova Y, Bashenkhaeva M, Galachyants Y, Petrova D, Tomberg I, Marchenkov A, Kopyrina L, Likhoshway Y. Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia. MICROBIAL ECOLOGY 2022; 84:958-973. [PMID: 34741646 DOI: 10.1007/s00248-021-01912-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, Nmin concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.
Collapse
Affiliation(s)
- Yulia Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Maria Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia.
| | - Yuri Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Darya Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Irina Tomberg
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Artyom Marchenkov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Liubov Kopyrina
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, 41 Lenin Ave, Yakutsk, 677980, Russia
| | - Yelena Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| |
Collapse
|
22
|
Osman OA, Andersson J, Martin-Sanchez PM, Eiler A. National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species (Batrachochytrium dendrobatidis -Bd), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA.
Collapse
|
23
|
Qi R, Xue N, Zhou X, Zhao L, Song W, Yang Y. Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types? MICROBIAL ECOLOGY 2022; 84:769-779. [PMID: 34686898 DOI: 10.1007/s00248-021-01902-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.
Collapse
Affiliation(s)
- Ran Qi
- Institute of Geological Survey, China University of Geosciences, Wuhan, 430074, China
- Command Center of Integrated Survey of Natural Resources, China Geological Survey, Beijing, 100055, China
| | - Nana Xue
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaobin Zhou
- Xinjiang Laboratory of Environmental Pollution and Ecological Remediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Li Zhao
- Xinjiang Laboratory of Environmental Pollution and Ecological Remediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wenjuan Song
- Xinjiang Laboratory of Environmental Pollution and Ecological Remediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- University of Chinese Academy of Science, Beijing, 100049, China.
| | - Yuyi Yang
- University of Chinese Academy of Science, Beijing, 100049, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| |
Collapse
|
24
|
Martínez-García S, Bunse C, Pontiller B, Baltar F, Israelsson S, Fridolfsson E, Lindh MV, Lundin D, Legrand C, Pinhassi J. Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent. Front Microbiol 2022; 13:834675. [PMID: 36212867 PMCID: PMC9533715 DOI: 10.3389/fmicb.2022.834675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction <3.0 μm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.
Collapse
Affiliation(s)
- Sandra Martínez-García
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
- *Correspondence: Sandra Martínez-García,
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Benjamin Pontiller
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Stina Israelsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Emil Fridolfsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Markus V. Lindh
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
25
|
Ou-Yang T, Yang SQ, Zhao L, Ji LL, Shi JQ, Wu ZX. Temporal heterogeneity of bacterial communities and their responses to Raphidiopsis raciborskii blooms. Microbiol Res 2022; 262:127098. [PMID: 35753182 DOI: 10.1016/j.micres.2022.127098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022]
Abstract
To elucidate the interspecies connectivity between cyanobacteria and other bacteria (noncyanobacteria), microbial diversity and composition were investigated through high-throughput sequencing (HTS) in a drinking water reservoir in Chongqing city, Southwest China, during Raphidiopsis raciborskii blooms. Significant temporal changes were observed in microbial community composition during the sampling period, primarily reflected by variations in relative bacterial abundance. The modularity analysis of the network demonstrated that the bacterial community forms co-occurrence/exclusion patterns in response to variations in environmental factors. Moreover, five modules involved in the dynamic phases of the R. raciborskii bloom were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups. The reservoir was eutrophic (i.e., the average concentrations of total nitrogen (TN) and total phosphorus (TP) were 2.32 and 0.07 mg L-1, respectively) during the investigation; however, Pearson's correlation coefficient showed that R. raciborskii was not significantly correlated with nitrogen and phosphorus. However, other environmental factors, such as water temperature, pH, and the permanganate index, were positively correlated with R. raciborskii. Importantly, Proteobacteria (α-, γ-Proteobacteria), Acidobacteria, Chloroflexi, and Firmicutes were preferentially associated with increased R. raciborskii blooms. These results suggested that the transition of R. raciborskii bloom-related microbial modules and their keystone species could be crucial in the development and collapse of R. raciborskii blooms and could provide a fundamental basis for understanding the linkage between the structure and function of the microbial community during bloom dynamics.
Collapse
Affiliation(s)
- Tian Ou-Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Song-Qi Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Lu Zhao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Lu-Lu Ji
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Jun-Qiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Zhong-Xing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China.
| |
Collapse
|
26
|
Hydroecology of Argyroneta aquatica’s Habitat in Hantangang River Geopark, South Korea. SUSTAINABILITY 2022. [DOI: 10.3390/su14094988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
The water spider (Argyroneta aquatic) is the only known spider to live a fully aquatic life. Therefore, it has been the subject of a series of studies on various aspects of its unique biology such as its reproductive behavior, sexual dimorphism, physiology, genetics, and silk. However, there have been relatively few studies on the hydroecology of where water spiders live. The water spider habitat in Eundae-ri, Yeoncheon is the only habitat for A. aquatica, a globally rare species, in South Korea. In this region, the water level of the wetland is automatically adjusted to groundwater owing to continued drying. Here, the surface water, wetland, and groundwater near the A. aquatica habitat were studied using hydrochemical, microbiological, and correlation analyses. The hydrochemical properties—water temperature, pH, electrical conductivity, dissolved oxygen (DO), oxidation reduction potential, and turbidity—of the surface water and wetland were similar. The Piper diagrams revealed that the wetlands, surface water, and most of the groundwater portrayed Ca-HCO3-type properties, whereas only areas where the water level of the wetland was controlled displayed Na-HCO3-type properties. Furthermore, the NO3 content was too low to be detected in the wetland, indicating clean and non-polluted water conditions; additionally, heavier oxygen-hydrogen isotopes were observed because these regions were climatically affected by the wetland. The dominant bacteria were Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Nitrospirae. The correlation analysis revealed that the major environmental control factors of the A. aquatica habitat were DO, temperature, and pH, and the related bacteria were Cyanobacteria, Actinobacteria, and Verrucomicrobia.
Collapse
|
27
|
Díaz-Torres O, Lugo-Melchor OY, de Anda J, Pacheco A, Yebra-Montes C, Gradilla-Hernández MS, Senés-Guerrero C. Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season. Front Microbiol 2022; 13:832477. [PMID: 35479621 PMCID: PMC9037096 DOI: 10.3389/fmicb.2022.832477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake's water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4 +, and NO3 -. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.
Collapse
Affiliation(s)
- Osiris Díaz-Torres
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - Ofelia Yadira Lugo-Melchor
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - José de Anda
- Departamento de Tecnologia Ambiental, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico
| | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Mexico
| | | | | | | |
Collapse
|
28
|
Spatio-Temporal Dynamics in Physico-Chemical Properties, Phytoplankton and Bacterial Diversity as an Indication of the Bovan Reservoir Water Quality. WATER 2022. [DOI: 10.3390/w14030391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The study aimed to investigate the physico-chemical properties as well as phytoplankton and bacterial community diversity of Bovan Lake reservoir in Serbia to gain insight into the seasonal dynamic of water quality. All analyses were performed at three localities and water depths in spring, summer, autumn, and winter 2019. Seven phytoplankton phyla comprising 139 taxa were detected at all three localities (Chlorophyta 58%, Bacillariophyta 14%, Cyanobacteria 9%, Chrysophyta 5%, Dinophyta 5%, Euglenophyta 5%, and Cryptophyta 4%). Winter 2019 was characterized by the presence of 36 unique species in all phyla except Euglenophyta. Bacterial diversity analyses showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia dominated the water intake locality at all three water depths (0.5, 10, and 20 m below the surface). In general, the physico-chemical parameters, phytoplankton, and bacterial community composition depended on the season and the water depth and showed that Bovan Lake was of satisfactory ecological status and water quality at all localities, and meets the needs for all intended purposes.
Collapse
|
29
|
Valadez-Cano C, Hawkes K, Calvaruso R, Reyes-Prieto A, Lawrence J. Amplicon-based and metagenomic approaches provide insights into toxigenic potential in understudied Atlantic Canadian lakes. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cyanobacterial blooms and their toxigenic potential threaten freshwater resources worldwide. In Atlantic Canada, despite an increase of cyanobacterial blooms in the last decade, little is known about the toxigenic potential and the taxonomic affiliation of bloom-forming cyanobacteria. In this study, we employed polymerase chain reaction (PCR) and metagenomic approaches to assess the potential for cyanotoxin and other bioactive metabolite production in Harvey Lake (oligotrophic) and Washademoak Lake (mesotrophic) in New Brunswick, Canada, during summer and early fall months. The PCR survey detected the potential for microcystin (hepatotoxin) and anatoxin-a (neurotoxin) production in both lakes, despite a cyanobacterial bloom only being visible in Washademoak. Genus-specific PCR associated microcystin production potential with the presence of Microcystis in both lakes. The metagenomic strategy provided insight into temporal variations in the microbial communities of both lakes. It also permitted the recovery of a near-complete Microcystis aeruginosa genome with the genetic complement to produce microcystin and other bioactive metabolites such as piricyclamide, micropeptin/cyanopeptolin, and aeruginosin. Our approaches demonstrate the potential for production of a diverse complement of bioactive compounds and establish important baseline data for future studies of understudied lakes, which are frequently affected by cyanobacterial blooms.
Collapse
Affiliation(s)
- Cecilio Valadez-Cano
- Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| | - Kristen Hawkes
- Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| | - Rossella Calvaruso
- Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| | - Janice Lawrence
- Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| |
Collapse
|
30
|
OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6551890. [DOI: 10.1093/femsec/fiac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 11/14/2022] Open
|
31
|
Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau. Toxins (Basel) 2021; 13:toxins13120894. [PMID: 34941731 PMCID: PMC8704429 DOI: 10.3390/toxins13120894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/13/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.
Collapse
|
32
|
Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
Collapse
Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
| |
Collapse
|
33
|
Bacterioplankton Community as a Biological Element for Reservoirs Water Quality Assessment. WATER 2021. [DOI: 10.3390/w13202836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Water Framework Directive (WFD) is used to evaluate the water quality of aquatic ecosystems. Phytoplankton is the only biological element considered in the reservoirs water quality assessment. In this study, we aimed to assess the use of the bacterioplankton community as an indicator of water quality, using a culture-independent assay (denaturing gradient gel electrophoresis, DGGE). Four Portuguese reservoirs (Miranda, Pocinho, Aguieira and Alqueva) were analysed in four periods (autumn 2018, spring and autumn 2019, and spring 2020). Bacterial total abundance had similar values for Miranda, Pocinho and Aguieira, and generally lower values for Alqueva. Diversity and richness values did not show a clear trend. Negative correlations were observed between some nutrients and the bacterial community. Overall, members of Actinobacteria, Bacteroidetes, Cyanobacteria, Nitrospirae and Proteobacteria were identified in all sampling sites. In Alqueva, no spatial, temporal or water body quality relationships with bacterial community were observed, which may be due to its higher size, low water velocity rate and higher residence times. However, in Miranda, Pocinho and Aguieira, a strong spatial and temporal bacterial community dynamic was observed. Furthermore, the presence of some species (e.g., Acinetobacter sp.) may reflect the poor water quality that was not detected by the WFD approach.
Collapse
|
34
|
Tardy V, Etienne D, Masclaux H, Essert V, Millet L, Verneaux V, Lyautey E. Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France). FEMS Microbiol Ecol 2021; 97:6362600. [PMID: 34472595 DOI: 10.1093/femsec/fiab126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/31/2021] [Indexed: 11/15/2022] Open
Abstract
Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.
Collapse
Affiliation(s)
- Vincent Tardy
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - David Etienne
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - Hélène Masclaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valentin Essert
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Laurent Millet
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valérie Verneaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Emilie Lyautey
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| |
Collapse
|
35
|
Chen YH, Chiang PW, Rogozin DY, Degermendzhy AG, Chiu HH, Tang SL. Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach. Commun Biol 2021; 4:996. [PMID: 34426638 PMCID: PMC8382752 DOI: 10.1038/s42003-021-02510-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/01/2021] [Indexed: 11/08/2022] Open
Abstract
Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.
Collapse
Affiliation(s)
- Yu-Hsiang Chen
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Denis Yu Rogozin
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - Andrey G Degermendzhy
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
36
|
Piel T, Sandrini G, Muyzer G, Brussaard CPD, Slot PC, van Herk MJ, Huisman J, Visser PM. Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms. Microorganisms 2021; 9:microorganisms9071495. [PMID: 34361929 PMCID: PMC8304526 DOI: 10.3390/microorganisms9071495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022] Open
Abstract
Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.
Collapse
Affiliation(s)
- Tim Piel
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Giovanni Sandrini
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Corina P. D. Brussaard
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands
| | - Pieter C. Slot
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Maria J. van Herk
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Petra M. Visser
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Correspondence: ; Tel.: +31-20-5257073
| |
Collapse
|
37
|
Shao K, Yao X, Wu Z, Jiang X, Hu Y, Tang X, Xu Q, Gao G. The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China. BMC Microbiol 2021; 21:179. [PMID: 34126927 PMCID: PMC8201733 DOI: 10.1186/s12866-021-02252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 11/19/2022] Open
Abstract
Background Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations. Results We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+ )were the dominant environmental drivers affecting the bacterial community variance. Conclusions The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02252-9.
Collapse
Affiliation(s)
- 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, 210008, Nanjing, China
| | - Xin Yao
- School of Environment and Planning, Liaocheng University, 252000, Liaocheng, China
| | - Zhaoshi Wu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - 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, 210008, Nanjing, 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, 210008, Nanjing, China
| | - Qiujin Xu
- Chinese Research Academy of Environmental Sciences, 100012, Beijing, 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, 210008, Nanjing, China.
| |
Collapse
|
38
|
Colman DR, Lindsay MR, Harnish A, Bilbrey EM, Amenabar MJ, Selensky MJ, Fecteau KM, Debes RV, Stott MB, Shock EL, Boyd ES. Seasonal hydrologic and geologic forcing drive hot spring geochemistry and microbial biodiversity. Environ Microbiol 2021; 23:4034-4053. [PMID: 34111905 DOI: 10.1111/1462-2920.15617] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/10/2021] [Accepted: 05/29/2021] [Indexed: 01/31/2023]
Abstract
Hot springs integrate hydrologic and geologic processes that vary over short- and long-term time scales. However, the influence of temporal hydrologic and geologic change on hot spring biodiversity is unknown. Here, we coordinated near-weekly, cross-seasonal (~140 days) geochemical and microbial community analyses of three widely studied hot springs with local precipitation data in Yellowstone National Park. One spring ('HFS') exhibited statistically significant, coupled microbial and geochemical variation across seasons that was associated with recent precipitation patterns. Two other spring communities, 'CP' and 'DS', exhibited minimal to no variation across seasons. Variability in the seasonal response of springs is attributed to differences in the timing and extent of aquifer recharge with oxidized near-surface water from precipitation. This influx of oxidized water is associated with changes in community composition, and in particular, the abundances of aerobic sulfide-/sulfur-oxidizers that can acidify waters. During sampling, a new spring formed after a period of heavy precipitation and its successional dynamics were also influenced by surface water recharge. Collectively, these results indicate that changes in short-term hydrology associated with precipitation can impact hot spring geochemistry and microbial biodiversity. These results point to potential susceptibility of certain hot springs and their biodiversity to sustained, longer-term hydrologic changes.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Annette Harnish
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Evan M Bilbrey
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Matthew J Selensky
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Randall V Debes
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Everett L Shock
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.,School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| |
Collapse
|
39
|
Pascault N, Rué O, Loux V, Pédron J, Martin V, Tambosco J, Bernard C, Humbert JF, Leloup J. Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions? ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:364-374. [PMID: 33763994 DOI: 10.1111/1758-2229.12944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Specific interactions have been highlighted between cyanobacteria and chemotrophic bacteria within the cyanosphere, suggesting that nutrients recycling could be optimized by cyanobacteria/bacteria exchanges. In order to determine the respective metabolic roles of the cyanobacterial and bacterial consortia (microbiome), a day-night metatranscriptomic analysis was performed on Dolichospermum sp. (N2 -fixer) and Microcystis sp. (non N2 -fixer) natural blooms occurring successively within a French peri-urban lake. The taxonomical and functional analysis of the metatranscriptoms have highlighted specific association of bacteria within the cyanosphere, driven by the cyanobacteria identity, without strongly modifying the functional composition of the microbiomes, suggesting functional redundancy within the cyanosphere. Moreover, the functional composition of these active communities was driven by the living mode. During the two successive bloom events, it appeared that NH4 + (newly fixed and/or allochthonous) was preferentially transformed into amino acids for the both the microbiome and the cyanobacteria, while phosphate metabolism was enhanced, suggesting that due to a high cellular growth, P limitation might take place within the cyanosphere consortium.
Collapse
Affiliation(s)
- Noémie Pascault
- UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, 78350, France
| | - Valentin Loux
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, 78350, France
| | - Jacques Pédron
- UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France
| | - Véronique Martin
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, 78350, France
| | - Jennifer Tambosco
- UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France
| | - Cécile Bernard
- UMR 7245 MCAM Muséum National d'Histoire Naturelle - CNRS, 75231 Paris Cedex 05, France
| | - Jean-François Humbert
- UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France
| | - Julie Leloup
- UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France
| |
Collapse
|
40
|
Verburg I, van Veelen HPJ, Waar K, Rossen JWA, Friedrich AW, Hernández Leal L, García-Cobos S, Schmitt H. Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment. Microorganisms 2021; 9:718. [PMID: 33807193 PMCID: PMC8065902 DOI: 10.3390/microorganisms9040718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022] Open
Abstract
This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as "target taxa"). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway. The study entailed a monthly sampling campaign along a wastewater pathway, and taxa identification through 16S rRNA amplicon sequencing. Results indicated that clinical and non-clinical wastewaters differed in their overall bacterial composition, but that target taxa were not enriched in clinical wastewater. This suggests that treatment of clinical wastewater before release into the wastewater system would only remove a minor part of the potential total pathogen load in wastewater treatment plants. Additional findings were that the relative abundance of most target taxa was decreased after wastewater treatment, yet all investigated taxa were detected in 68% of the treated effluent samples-meaning that these bacteria are continuously released into the receiving surface water. Temporal variation was only observed for specific taxa in surface water, but not in wastewater samples.
Collapse
Affiliation(s)
- Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - H. Pieter J. van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
| | - Karola Waar
- Izore, Centrum Infectieziekten Friesland, 8900 JA Leeuwarden, The Netherlands;
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Lucia Hernández Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
| | - Silvia García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (A.W.F.); (S.G.-C.)
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900 CC Leeuwarden, The Netherlands; (I.V.); (H.P.J.v.V.); (L.H.L.)
- Institute for Risk Assessment Sciences, Utrecht University, 3508 TD Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
| |
Collapse
|
41
|
Meziti A, Nikouli E, Hatt JK, Konstantinidis KT, Kormas KA. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. Environ Microbiol 2021; 23:3710-3726. [PMID: 33350070 DOI: 10.1111/1462-2920.15373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022]
Abstract
Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.
Collapse
Affiliation(s)
- A Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - E Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece
| |
Collapse
|
42
|
Wang M, Zhang H, Chen M, Yang L, Yang Y. Dark accelerates dissolved inorganic phosphorus release of high-density cyanobacteria. PLoS One 2020; 15:e0243582. [PMID: 33351804 PMCID: PMC7755282 DOI: 10.1371/journal.pone.0243582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 11/18/2022] Open
Abstract
Bloom-forming cyanobacteria dramatically influence nutrient cycling in eutrophic freshwater lakes. The phosphorus (P) assimilation and release of bloom-forming cyanobacteria significantly may also affect the phosphorus source and amounts in water. To understand the phosphorus release process of bloom-forming cyanobacteria below the accumulated surface and sedimentary bloom-forming cyanobacteria, the degradation of bloom-forming cyanobacteria dominated by Microcystis spp. at different cell density in the dark was investigated over a 25-day microcosm experiment. The dissolved inorganic phosphorus (DIP) and dissolved total phosphorus (DTP) contents increased with the increment of cyanobacterial density, and the dark status markedly increased the proportion of DIP in water during the decline period of bloom-forming cyanobacteria. Meanwhile, the process of cyanobacterial apoptosis accompanied by the changes of malondialdehyde (MDA) and phosphatase (AKP) contents, and the increases of superoxide dismutase (SOD) and catalase (CAT) activities of cyanobacteria in the dark, especially in low-density groups (5.23×108 cells L-1), which further affect the physicochemical water parameters. Moreover, the DIP release from high-density cyanobacteria (7.86×107 cells L-1~5.23×108 cells L-1) resulted from the relative abundance of organophosphorus degrading bacteria in the dark. Therefore, the fast decay of cyanobacteria in the dark could accelerate DIP release, the high DIP release amount from accumulated bloom-cyanobacteria provide adequate P quickly for the sustained growth of cyanobacteria.
Collapse
Affiliation(s)
- Mengmeng Wang
- State Key Laboratory of Pollution Control and Research Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Huifen Zhang
- State Key Laboratory of Pollution Control and Research Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Menggaoshan Chen
- State Key Laboratory of Pollution Control and Research Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Research Reuse, School of the Environment, Nanjing University, Nanjing, China
- * E-mail:
| | - Yichen Yang
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL, United States of America
| |
Collapse
|
43
|
Laanto E, Ravantti JJ, Sundberg LR. Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. Microorganisms 2020; 8:E1919. [PMID: 33276599 PMCID: PMC7761591 DOI: 10.3390/microorganisms8121919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.
Collapse
Affiliation(s)
- Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Janne J. Ravantti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland;
| |
Collapse
|
44
|
Beier S, Andersson AF, Galand PE, Hochart C, Logue JB, McMahon K, Bertilsson S. The environment drives microbial trait variability in aquatic habitats. Mol Ecol 2020; 29:4605-4617. [PMID: 33001506 DOI: 10.1111/mec.15656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023]
Abstract
A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.
Collapse
Affiliation(s)
- Sara Beier
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany.,Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Universités, CNRS, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Anders F Andersson
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Sorbonne Universités, CNRS, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Corentin Hochart
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Sorbonne Universités, CNRS, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Jürg B Logue
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
| | - Katherine McMahon
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin Madison, Madison, WI, USA
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
45
|
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.
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile. Microorganisms 2020; 8:microorganisms8071077. [PMID: 32698305 PMCID: PMC7409041 DOI: 10.3390/microorganisms8071077] [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] [Received: 06/24/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.
Collapse
|
48
|
Manna V, Malfatti F, Banchi E, Cerino F, De Pascale F, Franzo A, Schiavon R, Vezzi A, Del Negro P, Celussi M. Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters. Front Microbiol 2020; 11:1242. [PMID: 32582131 PMCID: PMC7296054 DOI: 10.3389/fmicb.2020.01242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022] Open
Abstract
Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L-1) and intense (10 μg of Chlorophyll a L-1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes' abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.
Collapse
Affiliation(s)
- Vincenzo Manna
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Department of Life Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Francesca Malfatti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Elisa Banchi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Federica Cerino
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Fabio De Pascale
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Annalisa Franzo
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Riccardo Schiavon
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Alessandro Vezzi
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| |
Collapse
|
49
|
Jankowiak JG, Gobler CJ. The Composition and Function of Microbiomes Within Microcystis Colonies Are Significantly Different Than Native Bacterial Assemblages in Two North American Lakes. Front Microbiol 2020; 11:1016. [PMID: 32547511 PMCID: PMC7270213 DOI: 10.3389/fmicb.2020.01016] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
The toxic cyanobacterium Microcystis is one of the most pervasive harmful algal bloom (HAB) genera and naturally occurs in large colonies known to harbor diverse heterotrophic bacterial assemblages. While colony-associated microbiomes may influence Microcystis blooms, there remains a limited understanding of the structure and functional potential of these communities and how they may be shaped by changing environmental conditions. To address this gap, we compared the dynamics of Microcystis-attached (MCA), free-living (FL), and whole water (W) microbiomes during Microcystis blooms using next-generation amplicon sequencing (16S rRNA), a predictive metagenome software, and other bioinformatic approaches. Microbiomes were monitored through high resolution spatial-temporal surveys across two North American lakes, Lake Erie (LE) and Lake Agawam (LA; Long Island, NY, United States) in 2017, providing the largest dataset of these fractions to date. Sequencing of 126 samples generated 7,922,628 sequences that clustered into 7,447 amplicon sequence variants (ASVs) with 100% sequence identity. Across lakes, the MCA microbiomes were significantly different than the FL and W fractions being significantly enriched in Gemmatimonadetes, Burkholderiaceae, Rhizobiales, and Cytophagales and depleted of Actinobacteria. Further, although MCA communities harbored > 900 unique ASVs, they were significantly less diverse than the other fractions with diversity inversely related to bloom intensity, suggesting increased selection pressure on microbial communities as blooms intensified. Despite taxonomic differences between lakes, predicted metagenomes revealed conserved functional potential among MCA microbiomes. MCA communities were significantly enriched in pathways involved in N and P cycling and microcystin-degradation. Taxa potentially capable of N2-fixation were significantly enriched (p < 0.05) and up to four-fold more abundant within the MCA faction relative to other fractions, potentially aiding in the proliferation of Microcystis blooms during low N conditions. The MCA predicted metagenomes were conserved over 8 months of seasonal changes in temperature and N availability despite strong temporal succession in microbiome composition. Collectively, these findings indicate that Microcystis colonies harbor a statistically distinct microbiome with a conserved functional potential that may help facilitate bloom persistence under environmentally unfavorable conditions.
Collapse
Affiliation(s)
- Jennifer G. Jankowiak
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| |
Collapse
|
50
|
Wang J, Yuan S, Tang L, Pan X, Pu X, Li R, Shen C. Contribution of heavy metal in driving microbial distribution in a eutrophic river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136295. [PMID: 31945533 DOI: 10.1016/j.scitotenv.2019.136295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 05/27/2023]
Abstract
Urban rivers represent an important source of freshwater. Accelerated urban development has resulted in imbalances in the water ecological environment and even eutrophication. Moreover, both natural and anthropogenic sources result in frequent heavy metal pollution in urban rivers. However, the combined impact of eutrophication and heavy metal pollution on the diversity and structure of the river microbial communities has not been adequately addressed. The microbial community distribution and predicted functions were examined in six water and sediment samples from the Laojingshui (LJS) River using metagenomic sequencing. The results showed that there were distinct differences in the microbial composition along the river. Redundancy analysis (RDA) revealed that the redox potential (Eh) was the most influential factor, explaining 76.5% of the variation (p = 0.002), and the heavy metals Zn and Cu explained 4.5 and 3.9%, respectively (p < 0.05). The results revealed that high nitrogen and phosphorus concentrations may have affected the proliferation of opportunistic plant species, such as Eichhornia crassipes, but Eh and heavy metals may have had greater impacts than N and P on the microorganisms in the water and sediment. The sensitivities of Deltaproteobacteria, Acidobacteria, Gemmatimonadetes and Nitrospira were most significant under Zn and Cu contamination when accompanied by eutrophic conditions. The expression ratio of the CYS (Cystain) gene might explain why the spatial distribution of each metal differed. This study suggests that heavy metals in eutrophication water continue to be the main factors determining the composition of microbial community, so the treatment of eutrophic water still needs to attach great importance to the complex pollution of heavy metals.
Collapse
Affiliation(s)
- Jingting Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Tang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xiangdong Pan
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xunchi Pu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Ran Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China.
| | - Chao Shen
- Chengdu Engineering Corporation Limited, Power China, Chengdu 610041, China
| |
Collapse
|