Article
Marine & Freshwater Biology
Anetta Ameryk, Janina Kownacka, Mariusz Zalewski, Kasia Piwosz
Summary: The Vistula Lagoon is a semi-closed basin in the southern coast of the Baltic Sea with a unique environment for both freshwater and marine bacteria. Salinity strongly influenced the abundance of marine bacterial groups (SAR11 clade I/II) with a distinct seasonal pattern, while freshwater bacterial groups (SAR11 clade IIIb, Limnohabitans, Burkholderiales) were more associated with other environmental factors like temperature and nutrients. The results suggest that the Vistula Lagoon is not ideal for marine bacteria, but freshwater bacteria are able to establish niches within this ecosystem.
ESTUARINE COASTAL AND SHELF SCIENCE
(2021)
Article
Microbiology
Eric W. Getz, V. Celeste Lanclos, Conner Y. Kojima, Chuankai Cheng, Michael W. Henson, Max Emil Schon, Thijs J. G. Ettema, Brant C. Faircloth, J. Cameron Thrash
Summary: Based on phylogenomics and gene sequence analysis, it was found that SAR11 subclade V is closely related to the common AEGEAN-169 group, supporting the argument that it represents a taxonomic family. Subclade V/AEGEAN-169 has metabolic differences compared to SAR11, which likely allow them to play different roles in their ecological niches.
Article
Multidisciplinary Sciences
Eleanor A. Sheridan, Jeremy A. Fonvielle, Samuel Cottingham, Yi Zhang, Thorsten Dittmar, David C. Aldridge, Andrew J. Tanentzap
Summary: Plastic debris pollutes freshwaters extensively, and the leachate from plastic shopping bags has a significant influence on microbial metabolism and bacterial biomass. Plastic pollution may stimulate aquatic food webs, suggesting possible strategies for pollution mitigation.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Yaling Su, Yingxun Du, Peng Xing
Summary: The study found that the light-to-nutrient conditions in alpine lakes can limit bacteria, with significant differences in environmental conditions between lakes above and below the treeline. Lakes above treeline exhibited phosphorus limitation, while lakes below treeline had reduced phosphorus limitation due to high allochthonous organic matter input.
Article
Microbiology
Pablo Aguilar, Irma Vila, Ruben Sommaruga
Summary: This study assessed the distribution patterns of bacteria in high elevation lakes and found a vertical spatial zonation of bacterial communities. The microdiversity was found to contribute to this pattern. These results provide insights into how high elevation aquatic ecosystems are affected by changing environmental conditions, especially when warming is amplified with elevation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Izabela Mujakic, Adrian- Stefan Andrei, Tanja Shabarova, Livia Kolesar Fecskeova, Michaela M. Salcher, Kasia Piwosz, Rohit Ghai, Michal Koblizek
Summary: Gemmatimonadota bacteria are widely distributed in natural environments, including soil and water bodies. Analysis of metagenomes from five freshwater lakes in central Europe revealed diverse Gemmatimonadota populations, some of which are closely associated with phytoplankton and possess unique mitochondrial assembly genes.
Article
Agriculture, Dairy & Animal Science
Yongzhi Zhang, Sen Feng, Fan Gao, Hao Wen, Lingyun Zhu, Meng Li, Yilong Xi, Xianling Xiang
Summary: This study investigated the relationship between Brachionus calyciflorus-associated bacteria and bacterioplankton communities in freshwater. The results showed significant differences between the two bacterial communities, with a lower diversity in the B. calyciflorus-associated bacteria. Environmental factors had some influence on the community composition of B. calyciflorus-associated bacteria, with Raoultella and Delftia being the dominant genera. This study expands our understanding of the interaction between zooplankton and bacteria.
Article
Biochemistry & Molecular Biology
Shaomei He, Alexandra M. Linz, Sarah L. R. Stevens, Patricia Q. Tran, Francisco Moya-Flores, Ben O. Oyserman, Jeffrey R. Dwulit-Smith, Katrina T. Forest, Katherine D. McMahon
Summary: Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. The study explored the diversity, distribution, and expression of opsin genes in freshwater lakes with different characteristics. The results showed that opsin genes occurred more frequently in clearwater lakes, and their distribution was influenced by lake optical properties and dissolved organic carbon (DOC) levels. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes. Overall, these findings highlight the importance of rhodopsin-based phototrophy in freshwater energy budgets.
Article
Microbiology
Vinicius S. S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. M. Chiriac, Michaela M. M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujcic, Maliheh Mehrshad, Vojtech Kasalicky, Adrian-Stefan Andrei, Jitka Jezberova, Jaromir Seda, Pavel Rychtecky, Petr Znachor, Karel Simek, Rohit Ghai
Summary: This study performed high-resolution sampling of the spring bloom in a freshwater reservoir and identified previously unknown microbial taxa using metagenome-assembled genomes. The recovered genomes provide insights into the distributional dynamics and doubling times of microbial lineages during the bloom. Additionally, the study uncovered the presence of aplastidic cryptophytes and giant viruses, offering new understanding of plankton dynamics.
Review
Water Resources
Yonas Getaneh, Wuletawu Abera, Assefa Abegaz, Lulseged Tamene
Summary: This study conducted an inventory of existing literature on freshwater lakes in Ethiopia, finding that most studies focus on hydrochemical and biological characteristics, with less attention given to physical structure and processes, as well as spatial and temporal dynamics. Future research should emphasize the relationship between catchment biophysical dynamics and lake hydrological characteristics.
JOURNAL OF HYDROLOGY-REGIONAL STUDIES
(2022)
Article
Environmental Sciences
Huimin Xu, Dayong Zhao, Jin Zeng, Zhigang Mao, Xiaohong Gu, Qinglong L. Wu
Summary: Aquaculture has significant impacts on freshwater lakes, particularly on plankton communities. In this study, the effects of aquaculture on water quality, plankton diversity, and plankton metacommunity co-occurrence patterns were examined in a shallow freshwater lake. The results showed that ecological aquaculture was more efficient in nitrogen removal than ecological restoration. Moreover, lower bacterioplankton diversity but higher phytoplankton and zooplankton diversity were observed in the ecological aquaculture and ecological restoration zones. The lower network connectivity of the plankton metacommunities in these zones suggested a possible lower resistance to future disturbance. Additionally, different mechanisms drove plankton communities of different trophic levels.
ENVIRONMENTAL POLLUTION
(2022)
Article
Ecology
Franziska Klotz, Katharina Kitzinger, David Kamanda Ngugi, Petra Busing, Sten Littmann, Marcel M. M. Kuypers, Bernhard Schink, Michael Pester
Summary: Deep oligotrophic lakes sustain large populations of Nitrososphaeria, which are the key ammonia oxidizers in this habitat. However, their impact on N-cycling in lakes has rarely been quantified. This study followed the Nitrososphaeria population in Lake Constance and demonstrated their important role in the nitrogen cycle of deep oligotrophic lakes.
Review
Environmental Sciences
Silvia Beatriz Alves Rolim, Bijeesh Kozhikkodan Veettil, Antonio Pedro Vieiro, Anita Baldissera Kessler, Clovis Gonzatti
Summary: Harmful algal blooms, especially cyanobacterial blooms, are occurring in many freshwater lakes worldwide, impacting public health and ecosystem integrity. To mitigate their negative effects, prediction, early detection, and monitoring of algal blooms are crucial. Remote sensing, including different platforms and AI-based algorithms, provides an effective and cost-efficient method for detecting and monitoring these events. Recent advancements in using UAV platforms equipped with sophisticated sensors have revolutionized the detection and monitoring of water quality. Predicting algal blooms based on AI methods will play a key role in mitigating eutrophication in the future.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Kim Vincent, Hannah Holland-Moritz, Adam J. Solon, Eli M. S. Gendron, Steven K. Schmidt
Summary: This study investigates the composition of bacterioplankton communities in alpine and subalpine lakes. The results show that there are differences in bacterial communities between the two types of lakes in the early summer, but these differences disappear by the end of the summer. Several environmental factors, including dissolved organic carbon, pH, chlorophyll-a, and total dissolved nitrogen, are found to be correlated with the community divergence in the early summer. The timing of increased hydrologic connections with the terrestrial environment, due to springtime snowmelt, may contribute to the observed patterns.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Maria-Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Summary: Pelagic microbes in lakes and oceans can be grouped into free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. This review identifies genomic traits that enable pelagic freshwater microbes to thrive in their habitat, by comparing the genetic differences between pelagic marine and freshwater microbes and also freshwater sediment microbes. Metabolic differences, including transport functions, environmental information processing, and electron transport chain components, are found in pelagic freshwater microbes. This review also discusses lineages and mechanisms involved in habitat transitions and describes the distribution, ecology, and genomic make-up of abundant freshwater prokaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Microbiology
Kasia Piwosz, Indranil Mukherjee, Michaela M. Salcher, Vesna Grujcic, Karel Simek
Summary: Phagotrophic protists play a crucial role in aquatic food webs, and microscopy-based molecular techniques such as CARD-FISH provide reliable ecological information on specific lineages. Recent findings challenge the simplistic notion that flagellates are predominantly bacterivores, revealing them to be omnivores ingesting prokaryotes and other protists. This suggests a need for an updated model of microbial food webs in pelagic environments, incorporating at least two additional trophic levels in the nanoplankton size fraction.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tanja Shabarova, Michaela M. Salcher, Petr Porcal, Petr Znachor, Jiri Nedoma, Hans-Peter Grossart, Jaromir Seda, Josef Hejzlar, Karel Simek
Summary: The study shows that flooding events result in washed-out organisms and increased nutrient load, but microbial communities can recover to predisturbance state within two weeks. However, reassembly of phytoplankton and zooplankton takes longer. Dissolved nutrient release is associated with inflow rates and community recovery.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Izabela Mujakic, Adrian- Stefan Andrei, Tanja Shabarova, Livia Kolesar Fecskeova, Michaela M. Salcher, Kasia Piwosz, Rohit Ghai, Michal Koblizek
Summary: Gemmatimonadota bacteria are widely distributed in natural environments, including soil and water bodies. Analysis of metagenomes from five freshwater lakes in central Europe revealed diverse Gemmatimonadota populations, some of which are closely associated with phytoplankton and possess unique mitochondrial assembly genes.
Article
Microbiology
Maria-Cecilia Chiriac, Paul-Adrian Bulzu, Adrian-Stefan Andrei, Yusuke Okazaki, Shin-ichi Nakano, Markus Haber, Vinicius Silva Kavagutti, Paul Layoun, Rohit Ghai, Michaela M. Salcher
Summary: The study explored the diversity and abundance of candidate phyla radiation (CPR) bacteria in freshwater lakes. By conducting deep metagenomic sequencing, the researchers recovered a high diversity of CPR genomes, which showed reduced metabolic capacities and potential lifestyles. The findings suggest that CPR bacteria have a wide range of potential strategies for survival and adaptation.
Article
Ecology
Karel Simek, Indranil Mukherjee, Tiberiu Szoke-Nagy, Markus Haber, Michaela M. Salcher, Rohit Ghai
Summary: Morphologically indistinguishable aplastidic cryptophytes were found to be ubiquitous and prominent protistan bacterivores in freshwater ecosystems, playing important roles in carbon flow. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts, and their diversity has been largely undiscovered.
Review
Microbiology
Maria-Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Summary: Pelagic microbes in lakes and oceans can be grouped into free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. This review identifies genomic traits that enable pelagic freshwater microbes to thrive in their habitat, by comparing the genetic differences between pelagic marine and freshwater microbes and also freshwater sediment microbes. Metabolic differences, including transport functions, environmental information processing, and electron transport chain components, are found in pelagic freshwater microbes. This review also discusses lineages and mechanisms involved in habitat transitions and describes the distribution, ecology, and genomic make-up of abundant freshwater prokaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Gianna Dirren-Pitsch, Dominique Buhler, Michaela M. Salcher, Barbara Bassin, Alizee Le Moigne, Martina Schuler, Jakob Pernthaler, Thomas Posch
Summary: Planktonic ciliate species are crucial components of freshwater food webs, but their high variability in 18S rDNA copy numbers makes quantification challenging. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) combines molecular identification and microscopic quantification, enabling the identification and quantification of planktonic ciliates in field samples and the study of their population dynamics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Vinicius S. S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. M. Chiriac, Michaela M. M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujcic, Maliheh Mehrshad, Vojtech Kasalicky, Adrian-Stefan Andrei, Jitka Jezberova, Jaromir Seda, Pavel Rychtecky, Petr Znachor, Karel Simek, Rohit Ghai
Summary: This study performed high-resolution sampling of the spring bloom in a freshwater reservoir and identified previously unknown microbial taxa using metagenome-assembled genomes. The recovered genomes provide insights into the distributional dynamics and doubling times of microbial lineages during the bloom. Additionally, the study uncovered the presence of aplastidic cryptophytes and giant viruses, offering new understanding of plankton dynamics.
Article
Multidisciplinary Sciences
David Kamanda Ngugi, Michaela M. Salcher, Adrian-Stefan Andrei, Rohit Ghai, Franziska Klotz, Maria-Cecilia Chiriac, Danny Ionescu, Petra Buesing, Hans-Peter Grossart, Peng Xing, John C. Priscu, Salmor Alymkulov, Michael Pester
Summary: A study has found that the species diversity of ammonia-oxidizing archaea (AOA) in freshwater is lower compared to marine environments. The research also reveals that an uncultured freshwater AOA, Candidatus Nitrosopumilus limneticus, evolved in European lakes 13 million years ago and has remained genetically stable. These findings provide insights into the genetic diversity and adaptive mechanisms of AOA in lakes.
Article
Ecology
Alizee Le Moigne, Florian Randegger, Anubhav Gupta, Owen L. L. Petchey, Jakob Pernthaler
Summary: Stochasticity plays a major role in compositional beta-diversity in communities formed under similar environmental conditions. The variability of individual physiological traits in the source community can lead to variable functional traits in the newly formed communities. We examined the degree of stochasticity during the initial assembly of bacterial communities and found high compositional variability and functional differences among them.
Article
Microbiology
Jakob Pernthaler, Natalia Krempaska, Alizee le Moigne
Summary: The bacterial community composition in 'lake snow' particles can vary greatly. The researchers hypothesized that particle-attached (PA) bacteria play a significant role in the small-scale spatial diversity of pelagic communities. The study found clear seasonal differences in the community composition and assembly of free-living (FL) bacteria, with high spatial beta diversity in PA bacteria. The genotypic heterogeneity of PA bacteria might affect the spatial distribution of rare metabolic traits.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Soil Science
Rong Sheng, Huifang Xu, Xiaoyi Xing, Wenzhao Zhang, Haijun Hou, Hongling Qin, Yi Liu, Limei Zhang, Yunting Fang, Jupei Shen, Jakob Pernthaler, Wenxue Wei, Baoli Zhu
Summary: The influence of parent materials on soil bacterial communities in agricultural soils was investigated. Different soil types were found to support distinct bacterial communities. The characteristics inherited from parent materials explained more of the variation in bacterial community structure than soil management variables and climate conditions.
Article
Ecology
Vinicius. S. S. Kavagutti, Maria-Cecilia Chiriac, Rohit Ghai, Michaela. M. M. Salcher, Markus Haber
Summary: The low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' are abundant in freshwater environments globally and have high levels of microdiversity, possibly due to predation pressure by phages. In this study, a novel species of the genus 'Ca. Planktophila' was isolated and used to cultivate the first two phages infecting this bacterial order. These phages have unique genomes and exhibit high levels of horizontal gene transfer.