ABSTRACT: A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5%) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: Ca. Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of Ca. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.
{"title":"16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds","authors":"Antti J. Rissanen, Moritz Buck, Sari Peura","doi":"10.3354/ame01983","DOIUrl":"https://doi.org/10.3354/ame01983","url":null,"abstract":"ABSTRACT: A putative novel methanotrophic genus, <i>Candidatus</i> Methylumidiphilus (<i>Methylococcales)</i>, was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with <i>Ca</i>. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as <i>Ca</i>. Methylumidiphilus (with completeness over 40% and contamination less than 5%) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: <i>Ca.</i> Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of <i>Ca</i>. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"122 4","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138495438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cecilia Alonso, Emiliano Pereira, Florencia Bertoglio, Miquel De Cáceres, Rudolf Amann
ABSTRACT: Increasing awareness of environmental impacts caused by anthropogenic activities highlights the need to determine indicators of environmental status that can be routinely assessed at large spatial and temporal scales. Microbial communities comprise the greatest share of biological diversity on Earth and can rapidly reflect recent environmental changes while providing a record of past events. However, they have rarely been targeted in the search for ecological indicators of habitat types, environmental conditions, or environmental changes. Here, as a proof of principle, we analysed the bacterioplankton community composition of 4 estuaries in North and South America, Europe, and Asia, and looked for indicators of groups of samples defined using partition techniques, according to primary physicochemical variables typically monitored to infer water quality. Indicator value analysis (IndVal) was conducted to identify indicator operational taxonomic units (OTUs; analogous to species in other fields of ecology) in each group. These bacterioplankton-based indicators exhibited a high capacity to predict the group membership of the samples within each estuary and to correctly assign the samples to the appropriate estuary in a combined data set, employing different machine learning techniques. The indicators were composed of OTUs belonging to several bacterial phyla, which responded significantly and differentially to the environmental variables used to define the groups of samples. Moreover, the predictive values of these bacterial indicators were generally higher than those of other biological assemblages commonly used for environmental monitoring. Therefore, this approach appears to be a promising tool to complement existing strategies for monitoring and conservation of aquatic systems worldwide.
{"title":"Bacterioplankton composition as an indicator of environmental status: proof of principle using indicator value analysis of estuarine communities","authors":"Cecilia Alonso, Emiliano Pereira, Florencia Bertoglio, Miquel De Cáceres, Rudolf Amann","doi":"10.3354/ame01979","DOIUrl":"https://doi.org/10.3354/ame01979","url":null,"abstract":"ABSTRACT: Increasing awareness of environmental impacts caused by anthropogenic activities highlights the need to determine indicators of environmental status that can be routinely assessed at large spatial and temporal scales. Microbial communities comprise the greatest share of biological diversity on Earth and can rapidly reflect recent environmental changes while providing a record of past events. However, they have rarely been targeted in the search for ecological indicators of habitat types, environmental conditions, or environmental changes. Here, as a proof of principle, we analysed the bacterioplankton community composition of 4 estuaries in North and South America, Europe, and Asia, and looked for indicators of groups of samples defined using partition techniques, according to primary physicochemical variables typically monitored to infer water quality. Indicator value analysis (<i>IndVal</i>) was conducted to identify indicator operational taxonomic units (OTUs; analogous to species in other fields of ecology) in each group. These bacterioplankton-based indicators exhibited a high capacity to predict the group membership of the samples within each estuary and to correctly assign the samples to the appropriate estuary in a combined data set, employing different machine learning techniques. The indicators were composed of OTUs belonging to several bacterial phyla, which responded significantly and differentially to the environmental variables used to define the groups of samples. Moreover, the predictive values of these bacterial indicators were generally higher than those of other biological assemblages commonly used for environmental monitoring. Therefore, this approach appears to be a promising tool to complement existing strategies for monitoring and conservation of aquatic systems worldwide.","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"125 s1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138495416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
: Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates — salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr) — or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.
{"title":"Substrate diversity affects carbon utilization rate and threshold concentration for uptake by natural bacterioplankton communities","authors":"J. Sjöstedt, UJ Wünsch, CA Stedmon","doi":"10.3354/ame01986","DOIUrl":"https://doi.org/10.3354/ame01986","url":null,"abstract":": Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates — salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr) — or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"12 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85965847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. Grabowska-Grucza, A. Bukowska, W. Siuda, R. Chróst, B. Kiersztyn
{"title":"Impact of increasing temperature on the taxonomic and metabolic structure of bacterial communities in a global warming context","authors":"K. Grabowska-Grucza, A. Bukowska, W. Siuda, R. Chróst, B. Kiersztyn","doi":"10.3354/ame01988","DOIUrl":"https://doi.org/10.3354/ame01988","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"12 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74747018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F. Panizzuti, S. Citterio, R. Gentili, A. Navone, P. Panzalis, I. Provera, S. Caronni
{"title":"Microalgal characterization during a mucilaginous event on deep gorgonian forests of Tavolara Punta Coda Cavallo MPA","authors":"F. Panizzuti, S. Citterio, R. Gentili, A. Navone, P. Panzalis, I. Provera, S. Caronni","doi":"10.3354/ame01991","DOIUrl":"https://doi.org/10.3354/ame01991","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"38 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84535254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
On 11 March 2011, a mega-earthquake followed by a huge tsunami hit a large area of the Pacific coast of Tohoku, Japan, and caused widespread disturbances in marine ecosystems; however, the impacts on virus−bacteria systems have not yet been elucidated. To investigate whether virus−bacteria interactions were affected by the earthquake and tsunami, we analyzed time series data of viral and bacterial abundances in Otsuchi Bay. Data were collected every 2 mo, from July 2011 to September 2015. Bacterial abundance exhibited a recurrent seasonal cycle with high abundance during the warm season. The seasonal trend of viruses generally followed that of the bacteria, yielding an average virus to bacteria ratio (VBR) of 10.8 ± 3.6 (mean ± SD; n = 432). A notable exception was found at the first 2 sampling times (July and September 2011) when the VBR was consistently low, with an average value of 5.9 ± 1.2 (n = 32). The average VBR during these time periods was substantially lower than the VBR observed in the same season of subsequent years. An analysis of the subset of data collected in the warm season of 2011 and 2012 revealed that the viral abundance and VBR were negatively correlated with turbidity. These results support the hypothesis that viruses were scavenged by non-host particles from the resuspended sediments and damaged catchment. The earthquake and tsunami thus exerted a prolonged impact, over several months, on the virus−bacteria dynamics in Otsuchi Bay.
{"title":"Disturbed virus–bacteria dynamics in the Otsuchi Bay (Japan) after the mega-earthquake and tsunami in March 2011","authors":"T. Nagata, Y. Yang, H. Fukuda","doi":"10.3354/ame01984","DOIUrl":"https://doi.org/10.3354/ame01984","url":null,"abstract":"On 11 March 2011, a mega-earthquake followed by a huge tsunami hit a large area of the Pacific coast of Tohoku, Japan, and caused widespread disturbances in marine ecosystems; however, the impacts on virus−bacteria systems have not yet been elucidated. To investigate whether virus−bacteria interactions were affected by the earthquake and tsunami, we analyzed time series data of viral and bacterial abundances in Otsuchi Bay. Data were collected every 2 mo, from July 2011 to September 2015. Bacterial abundance exhibited a recurrent seasonal cycle with high abundance during the warm season. The seasonal trend of viruses generally followed that of the bacteria, yielding an average virus to bacteria ratio (VBR) of 10.8 ± 3.6 (mean ± SD; n = 432). A notable exception was found at the first 2 sampling times (July and September 2011) when the VBR was consistently low, with an average value of 5.9 ± 1.2 (n = 32). The average VBR during these time periods was substantially lower than the VBR observed in the same season of subsequent years. An analysis of the subset of data collected in the warm season of 2011 and 2012 revealed that the viral abundance and VBR were negatively correlated with turbidity. These results support the hypothesis that viruses were scavenged by non-host particles from the resuspended sediments and damaged catchment. The earthquake and tsunami thus exerted a prolonged impact, over several months, on the virus−bacteria dynamics in Otsuchi Bay.","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"51 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90529595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Ma, C. Becker, L. Weber, C. Sullivan, B. Zgliczynski, S. Sandin, M. Brandt, Tb Smith, A. Apprill
{"title":"Biogeography of reef water microbes from within reef to global scales","authors":"L. Ma, C. Becker, L. Weber, C. Sullivan, B. Zgliczynski, S. Sandin, M. Brandt, Tb Smith, A. Apprill","doi":"10.3354/ame01985","DOIUrl":"https://doi.org/10.3354/ame01985","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"42 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80133347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Nitrate availability modulates induced defenses in Phaeocystis globosa against protozoan grazers","authors":"X. Wang, F. Yang, Y. Wang","doi":"10.3354/ame01989","DOIUrl":"https://doi.org/10.3354/ame01989","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"1 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77308143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Genitsaris, N. Stefanidou, U. Sommer, M. Moustaka-Gouni
{"title":"Diversity of taxon-specific traits of seasonally distinct unicellular eukaryotic assemblages in a eutrophic coastal area with marked plankton blooms","authors":"S. Genitsaris, N. Stefanidou, U. Sommer, M. Moustaka-Gouni","doi":"10.3354/ame01992","DOIUrl":"https://doi.org/10.3354/ame01992","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"42 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78540125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbial diversity in marine sediments of two hydrocarbon reservoir areas in the eastern Atlantic Ocean","authors":"X. Wei, L. Liu, X. Chen, G. Jin, M. Cai, Z. Qiu","doi":"10.3354/ame01987","DOIUrl":"https://doi.org/10.3354/ame01987","url":null,"abstract":"","PeriodicalId":8112,"journal":{"name":"Aquatic Microbial Ecology","volume":"35 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79132896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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