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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 2020; 86:AEM.00140-20. [PMID: 32169939 DOI: 10.1128/aem.00140-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022] Open
Abstract
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.
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Tromas N, Taranu ZE, Martin BD, Willis A, Fortin N, Greer CW, Shapiro BJ. Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria. Front Microbiol 2018; 9:438. [PMID: 29636727 PMCID: PMC5880894 DOI: 10.3389/fmicb.2018.00438] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/26/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering - in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering - such as competition between closely related taxa, or convergent trait evolution in distantly related taxa - in shaping particular traits in microbial communities.
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Affiliation(s)
- Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Zofia E Taranu
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, United States
| | - Amy Willis
- Department of Statistics, University of Washington, Seattle, WA, United States.,Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Nathalie Fortin
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
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The Limnohabitans Genus Harbors Generalistic and Opportunistic Subtypes: Evidence from Spatiotemporal Succession in a Canyon-Shaped Reservoir. Appl Environ Microbiol 2017; 83:AEM.01530-17. [PMID: 28842542 DOI: 10.1128/aem.01530-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
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Wang F, Li W, Zhang J, Qi W, Zhou Y, Xiang Y, Shi N. Characterization of suspended bacteria from processing units in an advanced drinking water treatment plant of China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:12176-12184. [PMID: 28353100 DOI: 10.1007/s11356-017-8874-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/20/2017] [Indexed: 06/06/2023]
Abstract
For the drinking water treatment plant (DWTP), the organic pollutant removal was the primary focus, while the suspended bacterial was always neglected. In this study, the suspended bacteria from each processing unit in a DWTP employing an ozone-biological activated carbon process was mainly characterized by using heterotrophic plate counts (HPCs), a flow cytometer, and 454-pyrosequencing methods. The results showed that an adverse changing tendency of HPC and total cell counts was observed in the sand filtration tank (SFT), where the cultivability of suspended bacteria increased to 34%. However, the cultivability level of other units stayed below 3% except for ozone contact tank (OCT, 13.5%) and activated carbon filtration tank (ACFT, 34.39%). It meant that filtration processes promoted the increase in cultivability of suspended bacteria remarkably, which indicated biodegrading capability. In the unit of OCT, microbial diversity indexes declined drastically, and the dominant bacteria were affiliated to Proteobacteria phylum (99.9%) and Betaproteobacteria class (86.3%), which were also the dominant bacteria in the effluent of other units. Besides, the primary genus was Limnohabitans in the effluents of SFT (17.4%) as well as ACFT (25.6%), which was inferred to be the crucial contributors for the biodegradable function in the filtration units. Overall, this paper provided an overview of community composition of each processing units in a DWTP as well as reference for better developing microbial function for drinking water treatment in the future.
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Affiliation(s)
- Feng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai, 200092, P. R. China
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Weiying Li
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai, 200092, P. R. China.
- Key Laboratory of Yangtze Aquatic Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China.
| | - Junpeng Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
- Key Laboratory of Yangtze Aquatic Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Wanqi Qi
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai, 200092, P. R. China
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Yanyan Zhou
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
- Key Laboratory of Yangtze Aquatic Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Yuan Xiang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai, 200092, P. R. China
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Nuo Shi
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
- Key Laboratory of Yangtze Aquatic Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
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Ye Q, Liu J, Du J, Zhang J. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea. Front Microbiol 2016; 6:1519. [PMID: 26779172 PMCID: PMC4705239 DOI: 10.3389/fmicb.2015.01519] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/17/2015] [Indexed: 01/17/2023] Open
Abstract
Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.
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Affiliation(s)
- Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University Shanghai, China
| | - Jianan Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University Shanghai, China
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University Shanghai, China
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Peerakietkhajorn S, Tsukada K, Kato Y, Matsuura T, Watanabe H. Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:364-72. [PMID: 25534397 DOI: 10.1111/1758-2229.12260] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/06/2014] [Accepted: 11/30/2014] [Indexed: 05/03/2023]
Abstract
The filter-feeding crustacean Daphnia is a key organism in freshwater ecosystems. Here, we report the effect of symbiotic bacteria on ecologically important life history traits, such as population dynamics and longevity, in Daphnia magna. By disinfection of the daphniid embryos with glutaraldehyde, aposymbiotic daphniids were prepared and cultured under bacteria-free conditions. Removal of bacteria from the daphniids was monitored by quantitative polymerase chain reaction for bacterial 16S rRNA gene. The population of aposymbiotic daphniids was reduced 10-folds compared with that of the control daphniids. Importantly, re-infection with symbiotic bacteria caused daphniids to regain bacteria and increase their fecundity to the level of the control daphniids, suggesting that symbiotic bacteria regulate Daphnia fecundity. To identify the species of symbiotic bacteria, 16S rRNA genes of bacteria in daphniids were sequenced. This revealed that 50% of sequences belonged to the Limnohabitans sp. of the Betaproteobacteria class and that the diversity of bacterial taxa was relatively low. These results suggested that symbiotic bacteria have a beneficial effect on D. magna, and that aposymbiotic Daphnia are useful tools in understanding the role of symbiotic bacteria in the environmental responses and evolution of their hosts.
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Affiliation(s)
- Saranya Peerakietkhajorn
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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7
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Hall AR, Corno G. Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater. FEMS Microbiol Ecol 2014; 90:168-74. [PMID: 25056916 DOI: 10.1111/1574-6941.12388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/24/2022] Open
Abstract
Interspecific microbial interactions are important for community structure, function and evolution, but it is not fully understood how interactions among bacterial species are influenced by some types of abiotic environmental variation, such as exposure to antibiotics. We tested for the effect of an antibiotic, tetracycline, on interspecific interactions in vitro among four species of aquatic bacteria isolated from European water bodies. Interactions among species in experimental microcosms containing artificial lake water (ALW) supplemented with glucose were largely competitive, as detected by comparing mixed cultures to pure cultures of their constituent species. Sublethal concentrations of tetracycline changed the relative competitive abilities of different species and revealed considerable variation in antibiotic sensitivity, but did not reduce the average strength of competition. Interspecific interactions at a given concentration were largely predictable from growth in pure cultures and indirect interactions with other species. These results suggest that antibiotics such as tetracycline may have important consequences for interactions among bacterial species, but in our experiments this was because species varied in their capacities for growth in the presence of tetracycline, rather than reduced competition at increasing tetracycline concentrations.
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Affiliation(s)
- Alex R Hall
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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8
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Paver SF, Youngblut ND, Whitaker RJ, Kent AD. Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes. Environ Microbiol 2014; 17:816-28. [PMID: 24912130 DOI: 10.1111/1462-2920.12529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/03/2014] [Indexed: 11/27/2022]
Abstract
Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.
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Affiliation(s)
- Sara F Paver
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA
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9
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Zimmermann J, Lott C, Weber M, Ramette A, Bright M, Dubilier N, Petersen JM. Dual symbiosis with co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent. Environ Microbiol 2014; 16:3638-56. [DOI: 10.1111/1462-2920.12427] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/31/2014] [Accepted: 02/09/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Judith Zimmermann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
| | - Christian Lott
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
- Elba Field Station; HYDRA Institute for Marine Sciences; Fetovaia Campo nell'Elba (LI) Italy
| | - Miriam Weber
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
- Elba Field Station; HYDRA Institute for Marine Sciences; Fetovaia Campo nell'Elba (LI) Italy
| | - Alban Ramette
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
| | - Monika Bright
- Department of Limnology and Oceanography; University of Vienna; Althanstrasse Vienna Austria
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
| | - Jillian M. Petersen
- Max Planck Institute for Marine Microbiology, Celsiusstrasse; Bremen Germany
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10
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Contrasting effects of singlet oxygen and hydrogen peroxide on bacterial community composition in a humic lake. PLoS One 2014; 9:e92518. [PMID: 24667441 PMCID: PMC3965437 DOI: 10.1371/journal.pone.0092518] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 02/24/2014] [Indexed: 11/24/2022] Open
Abstract
Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (1O2) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (14C-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased 1O2 and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized 1O2 exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to 1O2 but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to 1O2 exposure compared to free-living populations. These results imply that 1O2 acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.
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Jezbera J, Jezberová J, Kasalický V, Šimek K, Hahn MW. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by Reverse Line Blot Hybridization. PLoS One 2013; 8:e58527. [PMID: 23554898 PMCID: PMC3595293 DOI: 10.1371/journal.pone.0058527] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria. Instead, our observations suggest that the genus Limnohabitans, as well as its R-BT subgroup, represent ecologically heterogeneous taxa, which underwent pronounced ecological diversification.
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Affiliation(s)
- Jan Jezbera
- Biology Centre of the ASCR, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic.
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Kasalický V, Jezbera J, Hahn MW, Šimek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One 2013; 8:e58209. [PMID: 23505469 PMCID: PMC3591437 DOI: 10.1371/journal.pone.0058209] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/30/2013] [Indexed: 01/30/2023] Open
Abstract
Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.
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Affiliation(s)
- Vojtěch Kasalický
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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13
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Våge S, Storesund JE, Thingstad TF. Adding a cost of resistance description extends the ability of virus-host model to explain observed patterns in structure and function of pelagic microbial communities. Environ Microbiol 2013; 15:1842-52. [PMID: 23331773 DOI: 10.1111/1462-2920.12077] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 12/19/2012] [Indexed: 01/21/2023]
Abstract
By adding a generic description of cost of resistance (COR) to the existing 'killing-the-winner' model, we show how this expands the model's explanatory power to include rank-abundance relationships in the host population. The model can predict a counter-intuitive relationship previously suggested in the literature, where abundant viruses are associated with rare hosts and vice versa. The model explains the observed dominance of slow-growing prokaryotes as the result of successful defence strategies, rather than as dormancy of hosts lacking essential substrates. In addition to these important conceptual aspects, the model is able to reproduce realistic values for virus : host ratios and partitioning of bacterial production between predatory loss and viral lysis. A high COR is also shown to increase the community's richness and Shannon diversity index. This model thus not only couples life strategies at the cellular level with system properties, but it also links the two system level properties of biogeochemical flows and diversity to each other. The model operates with host groups, and consequences for biodiversity when interpreting these groups in terms of species and strains are discussed.
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Affiliation(s)
- Selina Våge
- Department of Biology, University of Bergen, Bergen, Norway.
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Kindaichi T, Nierychlo M, Kragelund C, Nielsen JL, Nielsen PH. High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants. Environ Microbiol 2013; 15:1821-31. [PMID: 23320853 DOI: 10.1111/1462-2920.12074] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 12/02/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022]
Abstract
Microbial communities are typically characterized by conditions of nutrient limitation so the availability of the resources is likely a key factor in the niche differentiation across all species and in the regulation of the community structure. In this study we have investigated whether four species exhibit any in situ short-term changes in substrate uptake pattern when exposed to variations in substrate and growth conditions. Microautoradiography was combined with fluorescence in situ hybridization to investigate in situ cell-specific substrate uptake profiles of four probe-defined coexisting species in a wastewater treatment plant with enhanced biological phosphorus removal. These were the filamentous 'Candidatus Microthrix' and Caldilinea (type 0803), the polyphosphate-accumulating organism 'Candidatus Accumulibacter', and the denitrifying Azoarcus. The experimental conditions mimicked the conditions potentially encountered in the respective environment (starvation, high/low substrate concentration, induction with specific substrates, and single/multiple substrates). The results showed that each probe-defined species exhibited very distinct and constant substrate uptake profile in time and space, which hardly changed under any of the conditions tested. Such niche partitioning implies that a significant change in substrate composition will be reflected in a changed community structure rather than the substrate uptake response from the different species.
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Affiliation(s)
- Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima 739-8527, Japan
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15
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Genome sequences of two freshwater betaproteobacterial isolates, Limnohabitans species strains Rim28 and Rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers. J Bacteriol 2013; 194:6302-3. [PMID: 23105051 DOI: 10.1128/jb.01481-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Betaproteobacterial genus Limnohabitans represents an important part of freshwater bacterioplankton. Here, we report genome sequences of two Limnohabitans isolates, Rim28 and Rim47. They contain a complete photosynthesis gene cluster, RuBisCO, CO dehydrogenase, ammonia monooxygenase, and sulfur-oxidizing genes, which indicates a great metabolic versatility of the Limnohabitans species.
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16
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Horňák K, Corno G. Every coin has a back side: invasion by Limnohabitans planktonicus promotes the maintenance of species diversity in bacterial communities. PLoS One 2012; 7:e51576. [PMID: 23251582 PMCID: PMC3520937 DOI: 10.1371/journal.pone.0051576] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/01/2012] [Indexed: 11/18/2022] Open
Abstract
One of the earliest challenges for ecologists has been to study the impact of invasive species on microbial communities. Although bacteria are fundamental in biological processes, current knowledge on invasion effects by aquatic non-pathogenic bacteria is still limited. Using pure cultures of diverse planktonic bacteria as model organisms at two different carbon concentration levels, we tested the response of an assembled community to the invasion by Limnohabitans planktonicus, an opportunistic bacterium, successful in freshwaters. The invader, introduced at the early stationary growth phase of the resident community, caused a strong decrement of the abundance of the dominant species. This was due to competition for nutrients and a potential allelopathic interaction. Simultaneously, resident species formerly unable to successfully compete within the community, thus potentially exposed to competitive exclusion, increased their abundances. The overall result of the invasion was preservation of species diversity, the higher the lower was the substrate content available. Our study provides new insights into bacterial invasions, offering an alternative interpretation of invasions for community ecology.
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Affiliation(s)
- Karel Horňák
- Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic.
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17
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Töpper B, Thingstad TF, Sandaa RA. Effects of differences in organic supply on bacterial diversity subject to viral lysis. FEMS Microbiol Ecol 2012; 83:202-13. [DOI: 10.1111/j.1574-6941.2012.01463.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 07/27/2012] [Accepted: 07/28/2012] [Indexed: 01/04/2023] Open
Affiliation(s)
- Birte Töpper
- Department of Biology; University of Bergen; Bergen; Norway
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18
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Jezbera J, Jezberová J, Koll U, Horňák K, Šimek K, Hahn MW. Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats. FEMS Microbiol Ecol 2012; 81:467-79. [PMID: 22452571 DOI: 10.1111/j.1574-6941.2012.01372.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/16/2012] [Accepted: 03/16/2012] [Indexed: 12/22/2022] Open
Abstract
The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigated using fluorescence in situ hybridization. Moreover, seasonal development of Betaproteobacteria subgroups along the longitudinal axis of a reservoir was followed. Betaproteobacteria comprised on average 29.1%, Polynucleobacter 11.6%, P. necessarius 10.1%, P. acidiphobus/difficilis 0.5%, Limnohabitans 8.9%, and Methylophilus 0.9% of total bacterioplankton cells in the investigated habitats. Polynucleobacter necessarius and Limnohabitans coexisted in the majority of habitats but showed contrasting abundance patterns along the pH gradient of habitats (pH, 3.8-8.5). The observed distribution patterns could theoretically be explained by different preferences for substrate sources, that is, substances of humic origin in acidic waters and algal-derived substances in alkaline waters. However, substrate utilization patterns observed in laboratory experiments indicate no coherent group-specific differences in substrate preferences. Interestingly, similar distribution patterns were revealed for Limnohabitans and P. acidiphobus/difficilis, suggesting similar ecological adaptations of these distantly related taxa. Our findings further emphasize that at least two taxa of freshwater Betaproteobacteria represent ecologically diversified groups. Investigations at higher phylogenetic resolution are required for obtaining further insights into their ecology.
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Affiliation(s)
- Jan Jezbera
- Institute for Limnology, Austrian Academy of Sciences, Mondsee, Austria.
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19
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Selezska K, Kazmierczak M, Müsken M, Garbe J, Schobert M, Häussler S, Wiehlmann L, Rohde C, Sikorski J. Pseudomonas aeruginosa population structure revisited under environmental focus: impact of water quality and phage pressure. Environ Microbiol 2012; 14:1952-67. [DOI: 10.1111/j.1462-2920.2012.02719.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Liu Z, Huang S, Sun G, Xu Z, Xu M. Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China. FEMS Microbiol Ecol 2012; 80:30-44. [PMID: 22133045 DOI: 10.1111/j.1574-6941.2011.01268.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 11/04/2011] [Accepted: 11/21/2011] [Indexed: 11/28/2022] Open
Abstract
Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems.
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Affiliation(s)
- Zhenghui Liu
- College of Environmental Science and Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, China
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21
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Horňák K, Zeder M, Blom JF, Posch T, Pernthaler J. Suboptimal light conditions negatively affect the heterotrophy of Planktothrix rubescens but are beneficial for accompanying Limnohabitans spp. Environ Microbiol 2011; 14:765-78. [DOI: 10.1111/j.1462-2920.2011.02635.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Alga-derived substrates select for distinct Betaproteobacterial lineages and contribute to niche separation in Limnohabitans strains. Appl Environ Microbiol 2011; 77:7307-15. [PMID: 21873481 DOI: 10.1128/aem.05107-11] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the proportions of major Betaproteobacteria subgroups within bacterial communities in diverse nonaxenic, monospecific cultures of algae or cyanobacteria: four species of cryptophyta (genera Cryptomonas and Rhodomonas), four species of chlorophyta (genera Pediastrum, Staurastrum, and Chlamydomonas), and two species of cyanobacteria (genera Dolichospermum and Aphanizomenon). In the cryptophyta cultures, Betaproteobacteria represented 48 to 71% of total bacteria, the genus Limnohabitans represented 18 to 26%, and the Polynucleobacter B subcluster represented 5 to 16%. In the taxonomically diverse chlorophyta group, the genus Limnohabitans accounted for 7 to 45% of total bacteria. In contrast, cyanobacterial cultures contained significantly lower proportions of the Limnohabitans bacteria (1 to 3% of the total) than the cryptophyta and chlorophyta cultures. Notably, largely absent in all of the cultures was Polynucleobacter necessarius (Polynucleobacter C subcluster). Subsequently, we examined the growth of Limnohabitans strains in the presence of different algae or their extracellular products (EPP). Two strains, affiliated with Limnohabitans planktonicus and Limnohabitans parvus, were separately inoculated into axenic cultures of three algal species growing in an inorganic medium: Cryptomonas sp., Chlamydomonas noctigama, and Pediastrum boryanum. The Limnohabitans strains cocultured with these algae or inoculated into their EPP consistently showed (i) pronounced population growth compared to the control without the algae or EPP and (ii) stronger growth stimulation of L. planktonicus than of L. parvus. Overall, growth responses of the Limnohabitans strains cultured with algae were highly species specific, which suggests a pronounced niche separation between two closely related Limnohabitans species likely mediated by different abilities to utilize the substrates produced by different algal species.
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Jezbera J, Jezberová J, Brandt U, Hahn MW. Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification. Environ Microbiol 2011; 13:922-31. [PMID: 21208356 PMCID: PMC3087241 DOI: 10.1111/j.1462-2920.2010.02396.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The subspecies Polynucleobacter necessarius asymbioticus (> 99% 16S rRNA similarity) has a cosmopolitan distribution and a ubiquitous occurrence in lentic freshwater habitats. We tested if the observed ubiquity of these free-living planktonic freshwater bacteria results from a euryoecious (generalist) adaptation of P. n. asymbioticus strains, or from ecological diversification within the subspecies. We developed a reverse line blot hybridization assay enabling the cultivation-independent detection of 13 groups within the subspecies in environmental samples. A set of 121 lentic freshwater habitats, spanning a broad variety of habitat types (e.g. pH levels ranging from 3.8 to 8.5) was investigated for the presence of these 13 P. n. asymbioticus groups. Statistical analyses of the reverse line blot hybridization detections revealed pronounced differences in habitat preferences of several of the groups. Their preferences differed regarding pH, conductivity, dissolved organic carbon and oxygen concentration of habitats. For some groups, differences in environmental preferences resulted even in complete niche separation between them. The revealed differences in habitat preferences suggest that the previously reported ubiquity of P. n. asymbioticus results from ecological diversification within the taxon and not from generalist adaptation of strains.
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Affiliation(s)
- Jan Jezbera
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria.
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24
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Newton RJ, McMahon KD. Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environ Microbiol 2010; 13:887-99. [PMID: 21138514 DOI: 10.1111/j.1462-2920.2010.02387.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic Lake Mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). Microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (BCC) change or community activity response (assessed via alkaline phosphatase activity, APA) relative to the controls during any season. Treatments enriched with carbon- and nitrogen-containing compounds resulted in a dramatic BCC change and a large APA increase in the autumn and spring seasons, but only treatments receiving carbon, nitrogen and phosphorus (CNP) exhibited similar responses in the summer season. Despite the fact that the amendments created similar CNP concentration conditions across seasons, the BCC following amendment greatly varied among seasons. 16S rRNA gene sequence analysis indicated that many common freshwater bacterial lineages from the Alpha- and Betaproteobacteria class and Bacteroidetes phylum were favoured following nutrient (CNP) addition, but individual taxa were generally not favoured across all seasons. Targeted quantitative PCR analysis revealed that the abundance of the Actinobacteria acIB1 cluster decreased in all microcosms during all three seasons, while the Flavobacterium aquatile (spring) and ME-B0 (summer) clusters of Bacteroidetes increased following CNP addition. These results suggest a particular bacterial group is not universally favoured by increased nutrient loads to a lake; therefore, efforts to predict which bacteria are involved in nutrient cycling during these periods must take into account the seasonality of freshwater bacterial communities.
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Affiliation(s)
- Ryan J Newton
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Kasalický V, Jezbera J, Šimek K, Hahn MW. Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2710-2714. [PMID: 20061501 DOI: 10.1099/ijs.0.018952-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, II-B4(T) and II-D5(T), isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(18 : 1)ω7c/C(18 : 1)ω6c and C(12 : 0). Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA-DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5(T) (=DSM 21594(T) =CIP 109844(T)), and Limnohabitans parvus sp. nov., with the type strain II-B4(T) (=DSM 21592(T) =CIP 109845(T)). The description of the genus Limnohabitans is emended accordingly.
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Affiliation(s)
- Vojtěch Kasalický
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Jan Jezbera
- Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Karel Šimek
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
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Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J, Šimek K. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 60:1358-1365. [PMID: 19671731 DOI: 10.1099/ijs.0.013292-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A chemo-organotrophic, aerobic, facultatively anaerobic, non-motile strain, MWH-C5(T), isolated from the water column of the oligomesotrophic Lake Mondsee (Austria), was characterized phenotypically, phylogenetically and chemotaxonomically. The predominant fatty acids of the strain were C(16 : 1)omega7c/omega6c, C(16 : 0), C(12 : 1) and C(8 : 0)-3OH, the major quinone was ubiquinone Q-8 and the G+C content of the DNA of the strain was 55.5 mol%. 16S rRNA gene similarity to the closest related type strains was 96.6 % (Curvibacter delicatus LMG 4328(T)) and 95.7 % (Rhodoferax fermentans FR3(T)). Phylogenetic analysis of 16S rRNA gene sequences revealed the affiliation of the strain with the family Comamonadaceae (Betaproteobacteria); however, the phylogenetic position of the strain did not support an affiliation to any previously described genus within this family. A family-wide comparison of traits revealed that the strain possesses a unique combination of DNA G+C content, major fatty acids and major 3-hydroxy fatty acid. Furthermore, the strain differs in several traits from the closest related genera. Based on the phylogeny of the strain and differences from closely related genera, we propose to establish the new genus and species Limnohabitans curvus gen. nov., sp. nov. to accommodate this strain. The type strain of Limnohabitans curvus is MWH-C5(T) (=DSM 21645(T) =CCUG 56720(T)). The type strain is closely related to a large number of uncultured bacteria detected by cultivation-independent methods in various freshwater systems.
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Affiliation(s)
- Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Vojtěch Kasalický
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Jan Jezbera
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Brandt
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Jitka Jezberová
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Karel Šimek
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
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