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Wang Y, Zhou P, Zhou W, Huang S, Peng C, Li D, Li G. Network Analysis Indicates Microbial Assemblage Differences in Life Stages of Cladophora. Appl Environ Microbiol 2023; 89:e0211222. [PMID: 36880773 PMCID: PMC10057885 DOI: 10.1128/aem.02112-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Cladophora represents a microscopic forest that provides many ecological niches and fosters a diverse microbiota. However, the microbial community on Cladophora in brackish lakes is still poorly understood. In this study, the epiphytic bacterial communities of Cladophora in Qinghai Lake were investigated at three life stages (attached, floating, and decomposing). We found that in the attached stage, Cladophora was enriched with chemoheterotrophic and aerobic microorganisms, including Yoonia-Loktanella and Granulosicoccus. The proportion of phototrophic bacteria was higher in the floating stage, especially Cyanobacteria. The decomposing stage fostered an abundance of bacteria that showed vertical heterogeneity from the surface to the bottom. The surface layer of Cladophora contained mainly stress-tolerant chemoheterotrophic and photoheterotrophic bacteria, including Porphyrobacter and Nonlabens. The microbial community in the middle layer was similar to that of floating-stage Cladophora. Purple oxidizing bacteria were enriched in the bottom layer, with Candidatus Chloroploca, Allochromatium, and Thiocapsa as the dominant genera. The Shannon and Chao1 indices of epibiotic bacterial communities increased monotonically from the attached stage to the decomposing stage. Microbial community composition and functional predictions indicate that a large number of sulfur cycle-associated bacteria play an important role in the development of Cladophora. These results suggest that the microbial assemblage on Cladophora in a brackish lake is complex and contributes to the cycling of materials. IMPORTANCE Cladophora represents a microscopic forest that provides many ecological niches fostering a diverse microbiota, with a complex and intimate relationship between Cladophora and bacteria. Many studies have focused on the microbiology of freshwater Cladophora, but the composition and succession of microorganisms in different life stages of Cladophora, especially in brackish water, have not been explored. In this study, we investigated the microbial assemblages in the life stages of Cladophora in the brackish Qinghai Lake. We show that heterotrophic and photosynthetic autotrophic bacteria are enriched in attached and floating Cladophora, respectively, whereas the epiphytic bacterial community shows vertical heterogeneity in decomposing mats.
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Affiliation(s)
- Yuming Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Panpan Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Weicheng Zhou
- College of Chemistry, Biology and Environmental Engineering, Xiangnan University, Chenzhou, People’s Republic of China
| | - Shun Huang
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Genbao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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Guo L, Dai L, Zheng J, Zhou W, Peng C, Li D, Li G. Environmental factors associated with the filamentous green algae Cladophora blooms: A mesocosm experiment in a shallow eutrophic lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 313:114977. [PMID: 35367675 DOI: 10.1016/j.jenvman.2022.114977] [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: 01/06/2022] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
The process of ecological restoration in eutrophic lakes, often results in the blooming of the filamentous green algae Cladophora. This consequently affects the growth of submerged plants and the restoration of vegetation. However, the blooming process of Cladophora and the environmental factors affecting their growth are poorly understood. This has become a difficult problem in the management of lakes. The study therefore focused on succession process of Cladophora blooms and their driving factors through mesocosm experiments in Caohai Lake. The results of our experiment indicated that Cladophora growth was mainly affected by water temperature, turbidity and soluble reactive phosphorus concentration of the habitat where Elodea nuttallii and Cladophora coexist. Nuisance Cladophora was mainly affected by turbidity (>19.24 NTU) when the water temperature was above 15.7 °C. With increasing Cladophora biomass and decreasing turbidity (<4.88 NTU), Cladophora biomass accumulation was mainly limited by the soluble reactive phosphorus concentration (<3.2 μg/L). Recorded turbidity range of 9.54-13.19 NTU was found to cause dramatic changes in the biomass of Cladophora. The results also showed that the outbreak of Cladophora blooms was mainly attributed to turbidity when the water temperature was appropriate in eutrophic lakes. These findings suggest that successful management efforts should strengthen the monitoring of transparency change in addition to controlling the phosphorus concentration to limit the Cladophora overgrowth on lake ecological restoration.
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Affiliation(s)
- Liangliang Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Key Laboratory of Geospatial Technology for Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng, 475004, China
| | | | - Jiaoli Zheng
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Weicheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chengrong Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Dunhai Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Genbao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Environmental Factors Drive Periphytic Algal Community Assembly in the Largest Long-Distance Water Diversion Channel. WATER 2022. [DOI: 10.3390/w14060914] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Periphytic algae exist widely in different waters. However, little is known about periphytic algae in long-distance water diversion channels across watersheds. We investigated the periphytic algae and the environmental factors at twenty sampling sites in the middle route of the South-to-North Water Diversion Project (MRP). The dominant species were Desmodesmus intermedius (Hegewald), Calothrix thermalis (Bornet & Flahault), Calothrix parietina (Bornet & Flahault) and Leptolyngbya benthonica (Anagnostidis) (dominance > 0.02) as measured in a whole year. Habitat heterogeneity in the MRP led to lower spatial heterogeneity and higher temporal heterogeneity of the periphytic algal community. Stochastic processes are the major process in periphytic community assembly. In deterministic processes, homogeneous selection had the major role in structuring the periphytic community, whereas the role of heterogeneous selection was less significant. In stochastic processes, dispersal limitations had the major role in structuring the periphytic community, whereas the role of homogenizing dispersal and drift were less significant. The variation in total nitrogen and total phosphorus promoted more stochastic processes (−1.96 < βNTI < 1.96). The variations in water temperature and water velocity promoted more heterogeneous selection (βNTI > 1.96). In integrating all of this empirical evidence, we explore the role of environmental factors in the action of ecological processes shaping thecommunity assembly of the periphytic algal community.
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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Sediment Microbial Diversity in Urban Piedmont North Carolina Watersheds Receiving Wastewater Input. WATER 2020. [DOI: 10.3390/w12061557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.
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Samad MS, Lee HJ, Cerbin S, Meima-Franke M, Bodelier PLE. Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes. Front Microbiol 2020; 11:582. [PMID: 32390961 PMCID: PMC7190982 DOI: 10.3389/fmicb.2020.00582] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.
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Affiliation(s)
- Md Sainur Samad
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, Gunsan, South Korea
| | - Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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Graham LE. Digging deeper: why we need more Proterozoic algal fossils and how to get them. JOURNAL OF PHYCOLOGY 2019; 55:1-6. [PMID: 30270424 DOI: 10.1111/jpy.12790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Known Proterozoic algal fossils raise compelling questions about the origin and diversification of cyanobacteria and eukaryotic algae, and their ecological influence in deep time. This Perspectives article describes particular examples of persistent evolutionary and biogeochemical issues whose resolution would be aided by additional algal fossil evidence from Proterozoic deposits, which have been the subjects of recent intensive study. New Proterozoic geosciences literature relevant to the early diversification of algae is surveyed. Previously underappreciated algal traits that might improve taxonomic attributions of fossil remains are highlighted. Processes that phycologists could use to improve detection of algal fossils are recommended. Potential geological sources of new Proterozoic fossils are suggested.
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Affiliation(s)
- Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
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Quigley CTC, Morrison HG, Mendonça IR, Brawley SH. A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome. JOURNAL OF PHYCOLOGY 2018; 54:653-664. [PMID: 29981525 DOI: 10.1111/jpy.12763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
While macroalgal microbiomes are the focus of many recent studies, there is little information about microbial spatial diversity across the thallus. Reliance on field material makes it difficult to discern whether recovered microbiomes belong to the host or its epiphytes, and technical comparisons of macroalgal samples for microbial studies are needed. Here, we use a common garden approach that avoids the problem of epiphytes, particularly at holdfasts, to examine the microbiome of Porphyra umbilicalis (strain Pum1). We used the V6 hypervariable region of the 16S rDNA with Illumina HiSeq sequencing and developed PNA clamps to block recovery of organelle V6 sequences. The common garden approach allowed us to determine differences in the microbiome at the holdfast versus blade margin. We found a notable increase in the relative abundance of Planctomycetes and Alphaproteobacteria at the holdfast, particularly of the possible symbiont Sulfitobacter sp. Nonadjacent 1.5 cm2 samples of blade margin had microbiomes that were not statistically different. The most abundant phylum in the overall microbiome was Proteobacteria, followed by Bacteroidetes. Because phycologists often work in remote sites, we compared three stabilization and preparation techniques and found silica gel desiccation/bead-beating and flash-freezing/lyophilization/bead-beating to be interchangeable. Core taxa (≥0.1% of sequences) across treatments were similar and accounted for ≥95% of all sequences. Finally, statistical conclusions for all comparisons were the same, regardless of which microbial community analysis tool was used: mothur or minimum entropy decomposition.
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Affiliation(s)
- Charlotte T C Quigley
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543, USA
| | - Inara R Mendonça
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
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Mathai PP, Dunn HM, Magnone P, Brown CM, Chun CL, Sadowsky MJ. Spatial and temporal characterization of epiphytic microbial communities associated with Eurasian watermilfoil: a highly invasive macrophyte in North America. FEMS Microbiol Ecol 2018; 94:5089967. [DOI: 10.1093/femsec/fiy178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/01/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- Prince P Mathai
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Hannah M Dunn
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Paolo Magnone
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Clairessa M Brown
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Chan Lan Chun
- Department of Civil Engineering, University of Minnesota, 1405 University Drive, Duluth, MN 55812, USA
- National Resources Research Institute, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave, St. Paul, MN 55108, USA
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