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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.
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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.
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2
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Wang L, Xiao Y, Lai W, Jia R, Deng Q, Wang X, Shi H, Yang Y, Zhang B. Micrococcus lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic algae. J Antibiot (Tokyo) 2024; 77:163-169. [PMID: 38148391 DOI: 10.1038/s41429-023-00690-3] [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: 08/21/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/28/2023]
Abstract
A novel actinobacterial strain, designated as JXJ CY 30 T, was isolated from the phycosphere of Microcystis aeruginosa FACHB-905 (Maf) collected from Lake Dianchi, China. The strain was a Gram-stain-positive, aerobic and coccus-shaped actinobacterium. It had alanine, glutamic acid, aspartic acid, and lysine in the peptidoglycan, and mannose, ribose and arabinose in its cell wall sugars, anteiso-C15:0 and iso-C15:0 as the main cellular fatty acids, MK-7 and MK-8 as the major respiratory quinones, and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, glycolipid, and an unidentified phospholipid as the polar lipids. The DNA G + C content was 73.08%. Its 16 S rRNA gene sequence shared 99.14%, and 98.75% similarities with Micrococcus flavus DSM 19079 T and M. porci KD337-16T, respectively, and ≤98.41% similarities with other type strains of the genus Micrococcus. It formed independent clade with M. flavus DSM 19079 T on the phylogenetic trees. The digital DNA-DNA hybridization and average nucleotide identity values between strain JXJ CY 30 T and M. flavus DSM 19079 T and M. porci KD337-16T were 48.0% and 92.1%, 25.5% and 83.2%, respectively. These data above indicated that strain JXJ CY 30 T represented a new species of the genus Micrococcus, and the species epithet is proposed as Micrococcus lacusdianchii sp. nov. (type strain JXJ CY 30 T = KCTC 49378 T = CGMCC 1.17508 T). Strain JXJ CY 30 T can potentially provide Maf with various nutrients such as available phosphorus and nitrogen, plant hormones, various vitamins and carotenoids for growth, while it was inhibited by metabolites from its symbiotic algae Maf.
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Affiliation(s)
- Le Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Wenxin Lai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Ru Jia
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Qinglin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Hongqiu Shi
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China
| | - Yiwen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China.
| | - Binghuo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332005, China.
- Jiujiang Key Laboratory for the Development and Utilization of Traditional Chinese Medicine resources in Northwest Jiangxi, Jiujiang, China.
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Xiao Y, Chen M, Chen J, Mao LN, Peng YR, Gui SS, Zhang BH. Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa. J Antibiot (Tokyo) 2022; 75:662-670. [PMID: 36167780 DOI: 10.1038/s41429-022-00568-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
A Gram-stain positive, aerobic, rod-shaped actinobacterial strain designated as JXJ CY 27-2T was isolated from the culture of Microcystis aeruginosa FACHB-905 (Maf) collected from Lake Kunming, southwest China. The isolate was catalase positive, oxidase negative, and able to grow at 10.0-44.0 °C, pH 5.0-10.0 and 0-5.0% NaCl. Based on the 16S rRNA gene sequences, JXJ CY 27-2T showed high similarities of 98.54-98.55% with Microbacterium invictum DSM 19600T, Microbacterium saccharophilum DSM 28107T, and Microbacterium aoyamense DSM 19461T, and less than 98.47% similarities with other members of the genus. Its major cellular fatty acids were anteiso-C17:0 and anteiso-C15:0. The predominant menaquinones were MK-11 and MK-12. The diagnostic diamino acid in the cell wall peptidoglycan was lysine. Whole cell sugars contained mannose, ribose, galactose, rhamnose and arabinose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, and an unidentified lipid. The DNA G + C content was 69.8%. The digital DNA-DNA hybridization and average nucleotide identity values between strain JXJ CY 27-2T and its three closest similar strains were 18.4-20.3% and 74.9-75.7%, respectively. Based on the above data, strain JXJ CY 27-2T was identified as a new species of the genus Microbacterium, for which the name Microbacterium kunmingensis sp. nov. is proposed. The type strain is JXJ CY 27-2T (=CGMCC 1.17506T = KCTC 49382T). Strain JXJ CY 27-2T could promote the growth of Maf by providing it with available phosphorus, nitrogen and probably other nutrients such as vitamins and indole-3-acetate.
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Affiliation(s)
- Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Min Chen
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Jian Chen
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Li-Na Mao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yi-Ru Peng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Shan-Shan Gui
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Bing-Huo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China.
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Zhang J, Nawaz MZ, Zhu D, Yan W, Alghamdi HA, Lu Z. Diversity, seasonal succession and host specificity of bacteria associated with cyanobacterial aggregates in a freshwater lake. ENVIRONMENTAL TECHNOLOGY & INNOVATION 2021; 24:101988. [DOI: 10.1016/j.eti.2021.101988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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Qi F, Jia Y, Mu R, Ma G, Guo Q, Meng Q, Yu G, Xie J. Convergent community structure of algal-bacterial consortia and its effects on advanced wastewater treatment and biomass production. Sci Rep 2021; 11:21118. [PMID: 34702904 PMCID: PMC8548336 DOI: 10.1038/s41598-021-00517-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Microalgal-bacterial consortium is an effective way to meet increasingly stringent standards in wastewater treatment. However, the mechanism of wastewater removal effect has not been properly explained in community structure by phycosphere. And little is known about that the concept of macroecology was introduced into phycosphere to explain the phenomenon. In the study, the algal-bacterial consortia with different ratios of algae and sludge were cultured in same aerobic wastewater within 48 h in photobioreactors (PSBRs). Community structure at start and end was texted by metagenomic analysis. Bray-Curtis similarities analysis based on microbial community showed that there was obvious convergent succession in all consortia, which is well known as "convergence" in macroecology. The result showed that Bray-Curtis similarities at End (overall above 0.88) were higher than these at Start (almost less than 0.66). In terms of community structure, the consortium with 5:1 ratio at Start are the more similar with the consortia at End by which the maximum removal of total dissolved nitrogen (TDN, 73.69%), total dissolved phosphorus (TDP, 94.40%) and NH3-N (93.26%) in wastewater treatment process and biomass production (98.2%) higher than other consortia, according with climax community in macroecology with the highest resource utilization than other communities. Therefore, the macroecology can be introduced into phycosphere to explain the consortium for advanced wastewater treatment and optimization community structure. And the study revealed a novel insight into treatment effect and community structure of algal-bacterial consortia for advanced wastewater treatment, a new idea for to shortening the culture time of consortium and optimize predicting their ecological community structure and predicting ecological community.
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Affiliation(s)
- Feng Qi
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Yantian Jia
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Ruimin Mu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China.
| | - Guixia Ma
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Qingyang Guo
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Qianya Meng
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Gejiang Yu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Jun Xie
- Shandong Provincial Eco-Environment Monitoring Center, Jinan, China
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Xie G, Tang X, Gong Y, Shao K, Gao G. How do Planktonic Particle Collection Methods Affect Bacterial Diversity Estimates and Community Composition in Oligo-, Meso- and Eutrophic Lakes? Front Microbiol 2020; 11:593589. [PMID: 33343534 PMCID: PMC7746777 DOI: 10.3389/fmicb.2020.593589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/17/2020] [Indexed: 12/26/2022] Open
Abstract
Particles are hotspots of bacterial growth and nutrient recycling in aquatic ecosystems. In the study of particle-attached (PA) and/or free-living (FL) microbial assemblages, the first step is to separate particles from their surrounding water columns. Widely used collection techniques are filtration using different pore size filters, and centrifugation; however, it is unclear how the bacterial diversity, bacterial community structure (BCS) and taxonomic composition of PA assemblages are affected by different particle collection methods. To address this knowledge gap, we collected planktonic particles from eutrophic Lake Taihu, mesotrophic Lake Tianmu, and oligotrophic Lake Fuxian in China, using filtration with five pore size of filters (20, 10, 8.0, 5.0, and 3.0 μm), and centrifugation. Bacterial communities were then analyzed using Illumina MiSeq sequencing of the 16S rRNA gene. We found that PA collection method affected BCS significantly in all lakes. Centrifugation yielded the highest species diversity and lowest mean percentage of photoautotrophic Cyanobacteria in Lake Taihu, but not in the other two lakes, thus highlighting the potential compatibility of this method in the study of PA assemblage in eutrophic lakes. The high bacterial diversity and low relative percentage of Cyanobacteria was in samples retained on 5.0 μm filters in all lakes. These results suggest that collecting PA samples in lakes using filters with 5.0 μm pore size is the preferred protocol, if species diversity and heterotrophic bacteria are the top research priorities, when comparing bacterial communities in different trophic lakes at the same time. The present study offers the possibility of collecting PA samples using unified methods in oligotrophic to eutrophic lakes.
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Affiliation(s)
- Guijuan Xie
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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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.
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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
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Wang H, Zhu R, Zhang X, Li Y, Ni L, Xie P, Shen H. Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake. AMB Express 2019; 9:170. [PMID: 31673822 PMCID: PMC6823470 DOI: 10.1186/s13568-019-0889-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.
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Tu J, Chen L, Gao S, Zhang J, Bi C, Tao Y, Lu N, Lu Z. Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies. Int J Mol Sci 2019; 20:ijms20205047. [PMID: 31614621 PMCID: PMC6829522 DOI: 10.3390/ijms20205047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).
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Affiliation(s)
- Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Liang Chen
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Shen Gao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Junyi Zhang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
- Wuxi Environmental Monitoring Center, Wuxi 210096, China.
| | - Changwei Bi
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yuhan Tao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Zhang W, Wang H, Zhang J, Chen J, Shen H, Xie P. Habitat species pools shape algal and bacterial communities and their correlations. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:275-286. [PMID: 30924315 DOI: 10.1111/1758-2229.12754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Understanding of community ecology is scale dependent. When the scale definition changes from subjectively defined "regional species pools" to "habitat species pools", heterogeneity differences occur for microbial communities. However, given the environmental gradients differences among habitats, responses of other organisms and interspecific correlations to habitat species pools may also be heterogeneous. This hypothesis is supported by our research about algal and bacterial communities among four different habitats in littoral zones. In our results, both the algal and bacterial community compositions varied along habitat species pools. Furthermore, at community level, significant correlation was only found between bacterioplankton and phytoplankton in pelagic habitat. And at individual level, the covariant trends between habitat generalists in algal and bacterial communities varied among habitats. Our results indicated that habitat-specific patterns can not only influence the habitat species pools, but also shape the interspecies interaction, and this should be considered in the further study of algae-bacterial correlation.
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Affiliation(s)
- Weizhen Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Wang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Jia Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong Shen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Ping Xie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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11
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Aguilar P, Dorador C, Vila I, Sommaruga R. Bacterial Communities Associated With Spherical Nostoc Macrocolonies. Front Microbiol 2019; 10:483. [PMID: 30949138 PMCID: PMC6437075 DOI: 10.3389/fmicb.2019.00483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/25/2019] [Indexed: 12/22/2022] Open
Abstract
Species of the genus Nostoc (Cyanobacteria) can form large colonies of up to several centimeters in diameter that may represent a unique habitat for bacteria in freshwaters. Bacteria inside the colony are probably segregated from the surrounding water and largely dependent on the metabolism of this primary producer. However, the existence of a specific bacterial community associated with free-living representatives of Nostoc from lakes and streams is unknown. Here, we studied large Nostoc spp. colonies (ca. 2-10 cm in diameter) from two adjacent, high altitude aquatic environments and assessed the diversity, and community composition of the bacterial community associated with the inner gelatinous matrix (GM). Further, we compared this community with that of the lake's littoral zone where the colonies live or with the outer layer (OL) of the colony in samples collected from a stream. Alpha bacterial diversity in the inner GM of the colonies from both sites was lower than in the littoral zone or than in the OL. Significant differences in community composition were found between the inner and the OL, as well as between the inner GM, and the littoral zone. Further, these differences were supported by the putative metabolic processes of the bacterial communities. Our results indicate the existence of a specific bacterial community inside macrocolonies of Nostoc spp. and also imply that the inner environment exerts a strong selection. Finally, these large colonies represent not only a unique habitat, but probably also a hotspot of bacterial activity in an otherwise oligotrophic environment.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering (CeBiB), Antofagasta, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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Li Q, Lin F, Yang C, Wang J, Lin Y, Shen M, Park MS, Li T, Zhao J. A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities. Front Microbiol 2018; 9:746. [PMID: 29731741 PMCID: PMC5919953 DOI: 10.3389/fmicb.2018.00746] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
Cyanobacterial blooms are worldwide issues of societal concern and scientific interest. Lake Taihu and Lake Dianchi, two of the largest lakes in China, have been suffering from annual Microcystis-based blooms over the past two decades. These two eutrophic lakes differ in both nutrient load and environmental parameters, where Microcystis microbiota consisting of different Microcystis morphospecies and associated bacteria (epibionts) have dominated. We conducted a comprehensive metagenomic study that analyzed species diversity, community structure, functional components, metabolic pathways and networks to investigate functional interactions among the members of six Microcystis-epibiont communities in these two lakes. Our integrated metagenomic pipeline consisted of efficient assembly, binning, annotation, and quality assurance methods that ensured high-quality genome reconstruction. This study provides a total of 68 reconstructed genomes including six complete Microcystis genomes and 28 high quality bacterial genomes of epibionts belonging to 14 distinct taxa. This metagenomic dataset constitutes the largest reference genome catalog available for genome-centric studies of the Microcystis microbiome. Epibiont community composition appears to be dynamic rather than fixed, and the functional profiles of communities were related to the environment of origin. This study demonstrates mutualistic interactions between Microcystis and epibionts at genetic and metabolic levels. Metabolic pathway reconstruction provided evidence for functional complementation in nitrogen and sulfur cycles, fatty acid catabolism, vitamin synthesis, and aromatic compound degradation among community members. Thus, bacterial social interactions within Microcystis-epibiont communities not only shape species composition, but also stabilize the communities functional profiles. These interactions appear to play an important role in environmental adaptation of Microcystis colonies.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feibi Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chen Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
| | - Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min S. Park
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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13
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Shi L, Huang Y, Zhang M, Shi X, Cai Y, Gao S, Tang X, Chen F, Lu Y, Kong F. Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free-living bacteria in the water column. Microbiologyopen 2018; 7:e00608. [PMID: 29573241 PMCID: PMC6291827 DOI: 10.1002/mbo3.608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 11/29/2022] Open
Abstract
Worldwide cyanobacterial blooms greatly impair ecosystems in many eutrophic lakes and impact the microbial environment. In particular, large cyanobacterial colonies that are buoyant on the water surface may provide a distinct habitat for bacteria from other small particles that are suspended stably in the water column. To test this hypothesis, bacterial communities (excluding cyanobacteria) attached to large particles dominated by cyanobacterial colonies (>120 μm, LA), small particles (3–36 μm, SA), and free‐living bacteria (0.2–3 μm, FL) were investigated monthly for a year in Lake Taihu, China. Results confirmed that the Shannon diversity index of LA was significantly lower than that of FL, which was lower than that of SA. Cytophagia and Alphaproteobacteria were specially enriched in LA. Although samples in each habitat collected during high‐ (May to November) and low‐bloom seasons (December to April) were separated, all samples in LA were clustered and separated from SA and FL, which were also clustered during the same sampling seasons. In addition, the bacterial communities in LA were correlated with nitrate level, whereas FL and SA were correlated with nitrate level and temperature. Mantel analysis revealed that bacterial composition significantly correlated with the cyanobacterial composition in LA and FL but not in SA. These results indicate that LA provides distinct niches to bacteria, whereas the differentiation of bacterial communities in FL and SA is seasonally dependent.
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Affiliation(s)
- Limei Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yaxin Huang
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China
| | - Shengling Gao
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Feizhou Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yaping Lu
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fanxiang Kong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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14
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Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 2017; 12:e0177488. [PMID: 28493994 PMCID: PMC5426677 DOI: 10.1371/journal.pone.0177488] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.
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Affiliation(s)
- Jessica M. Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Kristina D. Baker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Richard M. Zamor
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Steve Nikolai
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
- * E-mail:
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15
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Parulekar NN, Kolekar P, Jenkins A, Kleiven S, Utkilen H, Johansen A, Sawant S, Kulkarni-Kale U, Kale M, Sæbø M. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PLoS One 2017; 12:e0173408. [PMID: 28282404 PMCID: PMC5345797 DOI: 10.1371/journal.pone.0173408] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/19/2017] [Indexed: 11/19/2022] Open
Abstract
Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.
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MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Cyanobacteria/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Enzyme-Linked Immunosorbent Assay
- High-Throughput Nucleotide Sequencing
- Lakes/microbiology
- Microcystins/analysis
- Microcystis/genetics
- Microcystis/metabolism
- Norway
- Phytoplankton/genetics
- Phytoplankton/growth & development
- Proteobacteria/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Niranjan Nitin Parulekar
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
- * E-mail:
| | - Pandurang Kolekar
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Andrew Jenkins
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Synne Kleiven
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Hans Utkilen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Anette Johansen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Sangeeta Sawant
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mohan Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mona Sæbø
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
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16
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Zhu L, Zancarini A, Louati I, De Cesare S, Duval C, Tambosco K, Bernard C, Debroas D, Song L, Leloup J, Humbert JF. Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach. Front Microbiol 2016; 7:1662. [PMID: 27822204 PMCID: PMC5076464 DOI: 10.3389/fmicb.2016.01662] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/05/2016] [Indexed: 01/03/2023] Open
Abstract
To overcome the limitations associated with studying the interactions between bacterial communities (BCs) and cyanobacteria in natural environments, we compared the structural and functional diversities of the BCs associated with 15 non-axenic cyanobacterial strains in culture and two natural BCs sampled during cyanobacterial blooms. No significant differences in richness and diversity were found between the natural and cultivated BCs, although some of the cyanobacterial strains had been isolated 11 years earlier. Moreover, these BCs shared some similar characteristics, such as a very low abundance of Actinobacteria, but they display significant differences at the operational taxonomic unit (OTU) level. Overall, our findings suggest that BCs associated with cyanobacteria in culture are good models to better understand the interactions between heterotrophic bacteria and cyanobacteria. Additionally, BCs associated with heterocystous cyanobacterial strains cultivated in Z8X culture medium without nitrate (Aphanizomenon–Dolichospermum) demonstrated significant differences compared to BCs associated with non-heterocystous strains cultivated in Z8 culture medium (Planktothrix–Microcystis) in terms of their composition and their ability to utilize different carbon sources, suggesting the potential influence of cyanobacterial metabolism and/or culture media on associated BCs. Finally, half of the dominant OTUs in these BCs were specifically associated with cyanobacteria or other phytoplankton, whereas the remaining OTUs were generally associated with ecosystems containing high organic matter content, such as sludge or intestines.
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Affiliation(s)
- Lin Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesWuhan, China; UPMC-INRA, iEES-Paris UMR 7618Paris, France
| | | | - Imen Louati
- UPMC-INRA, iEES-Paris UMR 7618 Paris, France
| | | | - Charlotte Duval
- CNRS, MCAM, Muséum National d'Histoire Naturelle, UMR 7245, Sorbonne Universités Paris, France
| | | | - Cécile Bernard
- CNRS, MCAM, Muséum National d'Histoire Naturelle, UMR 7245, Sorbonne Universités Paris, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, Université de Clermont-Ferrand Clermont-Ferrand, France
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, China
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17
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Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Zhang YQ, Ai MJ, Hozzein WN, Li WJ. Modestobacter lacusdianchii sp. nov., a Phosphate-Solubilizing Actinobacterium with Ability to Promote Microcystis Growth. PLoS One 2016; 11:e0161069. [PMID: 27537546 PMCID: PMC4990248 DOI: 10.1371/journal.pone.0161069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/29/2016] [Indexed: 11/29/2022] Open
Abstract
A novel actinobacterium, designated strain JXJ CY 19T, was isolated from a culture mat of Microcystis aeruginosa FACHB-905 collected from Dianchi Lake, South-west China. 16S rRNA gene sequences comparison of strain JXJ CY 19T and the available sequences in the GenBank database showed that the strain was closely related to Modestobacter marinus 42H12-1T (99.1% similarity) and Modestobacter roseus KLBMP 1279T (99.0%). The isolate had meso-diaminopimelic in the cell wall with whole-cell sugars of mannose, rhamnose, ribose, glucose, galactose, and arabinose. The menaquinone detected was MK-9(H4), while the major cellular fatty acids include C17:1 ω8c, C15:0 iso, C15:1 iso G and C16:0 iso. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The DNA-DNA hybridization values between strains JXJ CY 19T and the closely related type strains Modestobacter marinus CGMCC 4.5581T and Modestobacter roseus NBRC 108673T were determined to be 50.8 ± 0.8% and 44.1 ± 1.7%, respectively. The DNA G+C content was 71.9 mol%. On the basis of the above taxonomic data and differences in physiological characters from the closely related type strains, strain JXJ CY 19T was recognized as a novel species of the genus Modestobacter, for which the name Modestobacter lacusdianchii sp. nov. (JXJ CY 19T = KCTC 39600T = CPCC 204352T) is proposed. The type strain JXJ CY 19T can solubilize calcium phosphate tribasic (Ca3(PO4)2), phytin and L-α-phosphatidylcholine. The phosphate-solubilizing property of the novel actinobacterium could be a possible factor for the increase in growth of Microcystis aeruginosa FACHB-905 in ecosystem where the amount of available soluble phosphate is limited such as Dianchi Lake.
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Affiliation(s)
- Bing-Huo Zhang
- College of Life Science, Jiujiang University, Jiujiang, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Juan Cheng
- College of Life Science, Jiujiang University, Jiujiang, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Han-Quan Li
- College of Life Science, Jiujiang University, Jiujiang, PR China
| | - Jian-Yuan Yang
- College of Life Science, Jiujiang University, Jiujiang, PR China
| | - Dai-Ming Zha
- College of Life Science, Jiujiang University, Jiujiang, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Meng-Jie Ai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Wael N. Hozzein
- Bioproducts Research Chair (BRC), Zoology Department, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Eqypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
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18
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Briand E, Humbert JF, Tambosco K, Bormans M, Gerwick WH. Role of bacteria in the production and degradation of Microcystis cyanopeptides. Microbiologyopen 2016; 5:469-78. [PMID: 26918405 PMCID: PMC4905998 DOI: 10.1002/mbo3.343] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/18/2016] [Accepted: 01/27/2016] [Indexed: 02/03/2023] Open
Abstract
The freshwater cyanobacteria, Microcystis sp., commonly form large colonies with bacteria embedded in their mucilage. Positive and negative interactions between Microcystis species and their associated bacteria have been reported. However, the potential role of bacteria in the production and degradation of cyanobacterial secondary metabolites has not been investigated. In this study, a Microcystis‐associated bacterial community was isolated and added to the axenic M. aeruginosaPCC7806 liquid culture. After 3 years of cocultivation, we studied the bacterial genetic diversity adapted to the PCC7806 strain and compared the intra‐ and extracellular concentration of major cyanopeptides produced by the cyanobacterial strain under xenic and axenic conditions. Mass spectrometric analyses showed that the intracellular concentration of peptides was not affected by the presence of bacteria. Interestingly, the produced peptides were detected in the axenic media but could not be found in the xenic media. This investigation revealed that a natural bacterial community, dominated by Alpha‐proteobacteria, was able to degrade a wide panel of structurally varying cyclic cyanopeptides.
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Affiliation(s)
- Enora Briand
- UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, 35042, France.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093
| | | | | | - Myriam Bormans
- UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, 35042, France
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093
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19
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Li J, Zhang J, Liu L, Fan Y, Li L, Yang Y, Lu Z, Zhang X. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu. Sci Rep 2015; 5:15488. [PMID: 26503553 PMCID: PMC4621408 DOI: 10.1038/srep15488] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis.
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Affiliation(s)
- Junfeng Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Wuxi Environmental Monitoring Centre, Wuxi, China
| | - Liyang Liu
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yucai Fan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lianshuo Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Department of Biomedical Engineering, Peking University, Beijing, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
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20
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Cai H, Jiang H, Krumholz LR, Yang Z. Bacterial community composition of size-fractioned aggregates within the phycosphere of cyanobacterial blooms in a eutrophic freshwater lake. PLoS One 2014; 9:e102879. [PMID: 25144467 PMCID: PMC4140718 DOI: 10.1371/journal.pone.0102879] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/24/2014] [Indexed: 11/18/2022] Open
Abstract
Bacterial community composition of different sized aggregates within the Microcystis cyanobacterial phycosphere were determined during summer and fall in Lake Taihu, a eutrophic lake in eastern China. Bloom samples taken in August and September represent healthy bloom biomass, whereas samples from October represent decomposing bloom biomass. To improve our understanding of the complex interior structure in the phycosphere, bloom samples were separated into large (>100 µm), medium (10-100 µm) and small (0.2-10 µm) size aggregates. Species richness and library coverage indicated that pyrosequencing recovered a large bacterial diversity. The community of each size aggregate was highly organized, indicating highly specific conditions within the Microcystis phycosphere. While the communities of medium and small-size aggregates clustered together in August and September samples, large- and medium-size aggregate communities in the October sample were grouped together and distinct from small-size aggregate community. Pronounced changes in the absolute and relative percentages of the dominant genus from the two most important phyla Proteobacteria and Bacteroidetes were observed among the various size aggregates. Bacterial species on large and small-size aggregates likely have the ability to degrade high and low molecular weight compounds, respectively. Thus, there exists a spatial differentiation of bacterial taxa within the phycosphere, possibly operating in sequence and synergy to catalyze the turnover of complex organic matters.
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Affiliation(s)
- Haiyuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- * E-mail:
| | - Lee R. Krumholz
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhen Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton. PLoS One 2014; 9:e85950. [PMID: 24465807 PMCID: PMC3896425 DOI: 10.1371/journal.pone.0085950] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 12/10/2013] [Indexed: 11/25/2022] Open
Abstract
Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.
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Cyanobacterial toxin degrading bacteria: who are they? BIOMED RESEARCH INTERNATIONAL 2013; 2013:463894. [PMID: 23841072 PMCID: PMC3690202 DOI: 10.1155/2013/463894] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/21/2013] [Indexed: 11/17/2022]
Abstract
Cyanobacteria are ubiquitous in nature and are both beneficial and detrimental to humans. Benefits include being food supplements and producing bioactive compounds, like antimicrobial and anticancer substances, while their detrimental effects are evident by toxin production, causing major ecological problems at the ecosystem level. To date, there are several ways to degrade or transform these toxins by chemical methods, while the biodegradation of these compounds is understudied. In this paper, we present a meta-analysis of the currently available 16S rRNA and mlrA (microcystinase) genes diversity of isolates known to degrade cyanobacterial toxins. The available data revealed that these bacteria belong primarily to the Proteobacteria, with several strains from the sphingomonads, and one from each of the Methylobacillus and Paucibacter genera. Other strains belonged to the genera Arthrobacter, Bacillus, and Lactobacillus. By combining the ecological knowledge on the distribution, abundance, and ecophysiology of the bacteria that cooccur with toxic cyanobacterial blooms and newly developed molecular approaches, it is possible not only to discover more strains with cyanobacterial toxin degradation abilities, but also to reveal the genes associated with the degradation of these toxins.
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