Submit to Diversity Review for Diversity Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Diversity and Ecology of Freshwater Lake Microbial Communities

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Freshwater Biodiversity".

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 12639

Share This Special Issue

Special Issue Editor

Dr. Yulia Robertovna Zakharova

E-Mail Website
Guest Editor

Limnological Institute, Siberian Branch of the Russian Academy of Sciencesdisabled, Irkutsk, Russia
Interests: freshwater ecosystems; oligotrophic lakes; algo-bacterial communities; cold-adapted bacteria; phytoplankton; microbial ecology; molecular microbiology; taxonomic diversity; cultivation of diatoms; culture collections; metagenomic analysis; genome; transcriptome; microscopy

Special Issue Information

Dear Colleagues,

We are pleased to announce a forthcoming Special Issue of Diversity focused on freshwater lake microbial communities. Globally, freshwaters are scarce commodities and make up only 0.009% of the Earth’s total water. Natural freshwaters are found in rivers and lakes, having a unique microbial ecology. Microbial communities (bacteria, archaea, and microbial eukaryotes) significantly contribute to the biodiversity of aquatic ecosystems and play an important role in food webs and biogeochemical cycles. The role bacteria and other microorganisms play in ecosystems and in biogeochemical cycles has been thoroughly investigated. For instance, the concept of the microbial loop is well established in lakes, meaning that microorganisms in the pelagic zone play important roles as links between dissolved organic matter and higher trophic levels. This activity is, for example, contributing to the important role lakes play in the global carbon cycle through consumption and emission of carbon dioxide and thereby in the regulation of the global climate. However, in these studies, microbial communities were mainly tracked using large part measurements of activity and abundance, paying little attention to the role of diversity and the contribution of individual populations and taxa. The structure of microbial communities is affected by interspecies interactions and local physicochemical and regional conditions. Phytoplankton bloom is one of the major factors affecting the composition of bacterial communities. Co-occurrence and correlation patterns can be used to predict positive and negative ecological interactions between various species and environmental parameters in freshwater ecosystems.

Despite methodological developments that have led to an exponential increase in the amount of data over time, we still have only little knowledge of the diversity of freshwater bacteria, and few general patterns in diversity have emerged. Using molecular methods, which enables the study of unculturable microorganisms, new information regarding freshwater microbial ecology has emerged in recent times: there are more phylogenetic groups of bacteria than are observed by cultural methods; there is a unique and distinct bacterial group, which can be termed “typical freshwater bacteria”; marine–freshwater transitional populations exist in coastal waters. The need for further research is exemplified by some findings of bacterial alpha diversity that further indicate that microbial diversity may not always follow the same rules as in larger organisms, challenging some established textbook “truths” regarding what is influencing diversity in general. Much more research is needed for certain conclusions. Future work should also include the identification of the true (active) players and their possible importance for ecosystem functioning. This Special Issue is an exciting opportunity to combine and synthesize recent research on the biodiversity and structure of freshwater microbial communities, as well as patterns of coexistence of bacteria, microbial eukaryotes, and environmental factors.

Dr. Yulia Robertovna Zakharova
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

freshwater systems
ecology microbial diversity
interactions and structure
metagenomics
high-throughput sequencing
microscopy

Published Papers (8 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

28 pages, 7006 KiB

Open AccessArticle

Free-Living and Particle-Associated Microbial Communities of Lake Baikal Differ by Season and Nutrient Intake

by Maria Bashenkhaeva, Yelena Yeletskaya, Irina Tomberg, Artyom Marchenkov, Lubov Titova and Yuri Galachyants

Diversity 2023, 15(4), 572; https://doi.org/10.3390/d15040572 - 18 Apr 2023

Cited by 1 | Viewed by 1233

Abstract

In an aquatic ecosystem, the supply of nutrients is essential for the biogeochemical cycle, and it affects the taxonomic composition of the microbial communities. Here, by using high-throughput sequencing (HTS) of the 16S and 18S rRNA gene fragments, we compared free-living (FL) and particle-associated (PA) bacterial communities and microeukaryotic communities in the areas with different nutrient intakes in freshwater Lake Baikal during the ice-covered and summer periods. Samples were taken at the inflow of the Selenga River, which is the main tributary of the lake, and at several established coastal research stations. The metabolic potential of the bacterial communities was predicted using PICRUSt. Differences were found in both FL and PA communities of the river mouth compared to the photic zone of the lake. The composition of FL communities was significantly different between the sampling sites in the ice-covered period, which is most likely influenced by different hydrochemical conditions. In contrast, the PA communities were more similar during the ice-covered period, but they changed considerably from spring to summer and their diversity increased. The diversity of the microeukaryotic communities also increased in summer, which may have contributed to the increase in bacterial diversity. In co-occurrence networks analysis, the number of interconnected bacterial OTUs in FL exceeded those for PA. The FL communities were dominated by Actinobacteriota, while the major PA OTUs belonged to a mixed cluster, which were mainly assigned to the phyla Bacteroidota and Verrucomicrobiota. As a result, PA communities were enriched in pathways responsible for the metabolism of sulfur, fucose, cellulose and urea. Our results confirm the difference between the FL and PA bacterial communities in Lake Baikal. These results also highlight the complex pattern of interactions between bacteria and microeukaryotes in a natural freshwater ecosystem across spatial and temporal scales. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

21 pages, 2580 KiB

Open AccessArticle

Microeukaryotic Communities of the Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia

by Yuri Galachyants, Yulia Zakharova, Maria Bashenkhaeva, Darya Petrova, Liubov Kopyrina and Yelena Likhoshway

Diversity 2023, 15(3), 454; https://doi.org/10.3390/d15030454 - 18 Mar 2023

Cited by 1 | Viewed by 1181

Abstract

Currently, microeukaryotic communities of the freshwater arctic and subarctic ecosystems are poorly studied. Still, these are of considerable interest due to the species biogeography and autecology as well as global climate change. Here, we used high-throughput 18S rRNA amplicon sequencing to study the microeukaryotic communities of the large subarctic freshwater lakes Labynkyr and Vorota in Yakutia, Russia, during the end of the ice cover period, from April to June. By applying the statistical methods, we coupled the microeukaryotic community structure profiles with available discrete factor variables and hydrophysical, hydrochemical, and environmental parameters. The sub-ice layer and the water column communities were differentiated due to the temporal change in environmental conditions, particularly temperature regime and electric conductivity. Additionally, the community composition of unicellular eukaryotes in lakes Labynkyr and Vorota was changing due to seasonal environmental factors, with these alterations having similar patterns in both sites. We suggest the community developed in the sub-ice layer in April serves as a primer for summer freshwater microeukaryotes. Our results extend the current knowledge on the community composition and seasonal succession of unicellular eukaryotes within subarctic freshwater ecosystems. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

13 pages, 58986 KiB

Open AccessArticle

Under-Ice Development of Silica-Scaled Chrysophytes with Different Trophic Mode in Two Ultraoligotrophic Lakes of Yakutia

by Anna Bessudova, Alena Firsova, Yurij Bukin, Lubov Kopyrina, Yulia Zakharova and Yelena Likhoshway

Diversity 2023, 15(3), 326; https://doi.org/10.3390/d15030326 - 22 Feb 2023

Cited by 4 | Viewed by 1140

Abstract

Silica-scaled chrysophytes are a widespread group of microeukaryotes, an important component of aquatic habitats. They belong to different evolutionary lineages and they are characterized by the presence of siliceous scales, but differ in trophic mode. We studied the diversity of these organisms in different months of the ice cover period in two subarctic lakes of Yakutia, Labynkyr and Vorota. Silica-scaled chrysophytes, due to various trophic modes, have a competitive advantage in conditions of a long period of ice cover. Statistical analysis has shown the relationship between the relative abundance of mixotrophic and photoautotrophic representatives of silica-scaled chrysophytes with the thickness of the snow cover and the transparency of the ice. An increase in snow cover thickness and the process of melting ice with a decrease in its transparency reduce the relative abundance of photoautotrophic and mixotrophic species. Photoautotrophic representatives of silica-scaled chrysophytes begin to develop already in April, when a thick, solid, and transparent layer of ice and a small layer of snow were observed. During the research period, from April to June, the relative abundance of colorless heterotrophic silica-scaled chrysophytes genera Paraphysomonas and Lepidochromonas was more or less stable. A new species of Spiniferomonas heterospina sp. nov. has been discovered in Lake Labynkyr. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

15 pages, 3188 KiB

Open AccessArticle

Bacterial Communities in a Gradient of Abiotic Factors Near a Sulfide Thermal Spring in Northern Baikal

by Svetlana Chernitsyna, Irina Elovskaya, Tatyana Pogodaeva, Sergei Bukin, Aleksandra Zakharenko and Tamara Zemskaya

Diversity 2023, 15(2), 298; https://doi.org/10.3390/d15020298 - 17 Feb 2023

Cited by 3 | Viewed by 1479

Abstract

The structure and diversity of microbial communities developing in the combined gradient of temperature (44–19 °C), as well as concentration of oxygen (0–10 mg/L) and hydrogen sulfide (33–0.7 mg/L), were studied in the thermal sulfide spring on the coast of Northern Lake Baikal. The predominance of bacteria participating in sulfur and nitrogen cycles and significant changes in the composition of microbial communities were noted at changing physicochemical conditions. Thiovirga sp. (sulfur-oxidizing bacteria, up to 37%) and Azonexus sp. (nitrogen-fixing bacteria, up to 43%) were dominant at high temperatures and concentrations of hydrogen sulfide in two hydrotherms. In addition, a significant contribution of the Rhodocyclaceae family (up to 51%) which is involved in the denitrification processes, and Acetoanaerobium sp. (up to 20%) fixing carbon oxide were found in the spring water. In the stream, mainly oxygenic cyanobacteria (up to 56%) developed at a temperature of 33 °C, in the presence of hydrogen sulfide and oxygen. In addition, sulfur bacteria of the genus Thiothrix (up to 48%) found in epibiotic communities of benthic animals of Lake Baikal were present here. Thiothrix sp. formed massive fouling in the zone of mixing lake and thermal waters with a significant contribution of hydrogen-oxidizing bacteria of the genus Hydrogenophaga (up to 22.5%). As well as chemolitho- and phototrophic bacteria, chemoorganotrophs (phyla Firmicutes, Chloroflexi, Desulfobacterota, Nitrospirota, Fibrobacterota, etc.) have been identified in all communities. The chemical parameters of water in spring and coastal zones indicate a significant change in the composition of thermal waters occurring with the participation of diverse microbial communities that contribute to the assimilation of inorganic components of mineral thermal waters. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

26 pages, 6486 KiB

Open AccessArticle

Delimitation of Some Taxa of Ulnaria and Fragilaria (Bacillariophyceae) Based on Genetic, Morphological Data and Mating Compatibility

by Yulia Zakharova, Artyom Marchenkov, Darya Petrova, Yurij Bukin, Aleksey Morozov, Yekaterina Bedoshvili, Yulia Podunay, Olga Davidovich, Nikolai Davidovich, Alexander Bondar, Maria Kahlert and Yelena Likhoshway

Diversity 2023, 15(2), 271; https://doi.org/10.3390/d15020271 - 13 Feb 2023

Cited by 3 | Viewed by 1960

Abstract

Fragilaria and Ulnaria are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of rbcL and 18S rRNA genes revealed that baikalian F. radians clade was independent from the representatives of the genus from other localities. Among Ulnaria we found the following 18S rRNA phylogenetic tree groups at species level: U. acus, U. ulna and U. danica. Genetic distance between genera varied between 3.9–10.2% substitutions in rbcL gene and 3.2–11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of Ulnaria and Fragilaria in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into F. radians, U. acus and U. ulna together with U. danica. Strains of U. acus and U. danica from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the Fragilaria. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

20 pages, 2338 KiB

Open AccessArticle

Toxic Effect of Anionic Surfactants on Freshwater Sponge Lubomirskia baikalensis and Its Endosymbiotic Microalgae Chlorella sp.

by Alyona Alexandrovna Nikonova, Igor Borisovich Mizandrontsev, Boris Nikolaevich Bazhenov, Igor Veniaminovich Khanaev, Olesya Viktorovna Shabalina, Alexandra Alexandrovna Afanasyeva, Tatiana Nikolaevna Avezova, Anna Nikolaevna Chindyavskaya, Alexander Nikolaevich Bityutsky, Andrey Yurievich Kan, Leonid Gennadievich Karikh, Kristina Sergeevna Dubrova, Svetlana Semyonovna Vorobyeva and Olga Yurievna Glyzina

Diversity 2023, 15(1), 77; https://doi.org/10.3390/d15010077 - 06 Jan 2023

Cited by 4 | Viewed by 1838

Abstract

A number of reports on sponge diseases, including from Lake Baikal, have increased dramatically all over the world in recent years. Herewith, there are various hypotheses for sponge mortality. Lubomirskia baikalensis (phylum Porifera, order Spongillida) is a unique endemic freshwater sponge of Lake Baikal that contains a complex community of eukaryotic and prokaryotic endosymbiotic microorganisms. In this work, we present the first results for the effect of anionic surfactants viz. linear alkylbenzene sulphonates (LAS) at low 10 and 20 µg L⁻¹ concentrations on Baikal sponge species and their symbiotic community as an experimental model. A new toxicity test protocol under conditions close to natural is proposed. It uses the sponge amoebocytes called as SA1-cells, which contain eukaryotic green microalgae Chlorella sp. These SA1-cells are shown to be representative indicator in assessing the impact of anionic surfactants. The acute toxic effect resulted in 97–100% sponge cell death in less than 48 h, as well as 100% symbiotic microalgae Chlorella sp. death over 72 h was noted under LAS solution (20 μg L⁻¹) exposure during in vivo experiments. This includes the cell membrane fatty acid changes, change in the cell sizes, cell swelling, and lysis. Long term exposure to LAS solution (10 μg L⁻¹) reflected in cellular stress (oxidative stress) and accompanied by malondialdehyde formation (0.16–2.0 μg g⁻¹ of dry weight) during 14-day exposure was noted. Oxidative stress and mortality of L. baikalensis are associated with their low antioxidant activity. Trolox-equivalent antioxidant capacity (TEAC) found in the range from 0.00031 to 0.00077 Trolox equivalents for these freshwater sponges. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

17 pages, 14567 KiB

Open AccessArticle

Morphological Variability of Alveolophora antiqua from a Freshwater Early Miocene Paleolake in the Barguzin Valley (Baikal Rift Zone)

by Marina Usoltseva, Lyubov’ Titova, Abdulmonem Hassan, Sergei Rasskazov and Alexey Morozov

Diversity 2022, 14(12), 1075; https://doi.org/10.3390/d14121075 - 05 Dec 2022

Cited by 1 | Viewed by 1134

Abstract

Using scanning electron microscopy, the morphology of Alveolophora antiqua (Moisseeva) Moisseeva from the freshwater Early Miocene paleolake in the Barguzin Valley was studied. We extended the species diagnosis relative to features such as spines, structure of areolae, costae, alveolae, rimoportulae and the external opening of rimoportulae and show a wide morphological variability with regard to valve shape (round, oval, ovoid and triangular). The percentage of these shapes varied with the core depth. Oval valves dominated in lower layers, while triangular ones occur in upper layers. We propose that the shape variability of valves might be due a sharp short-term cooling event or polyploidization. The finding of A. antiqua in the Early Miocene deposits of the Barguzin Valley expands both the georaphic and stratigraphic ranges of this species. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Figure 1

19 pages, 20231 KiB

Open AccessArticle

Spatial Variations of Aquatic Bacterial Community Structure and Co-Occurrence Patterns in a Coal Mining Subsidence Lake

by Tingyu Fan, Wangkai Fang, Yifan Zhao, Akang Lu, Shun Wang, Xingming Wang, Liangji Xu, Xiangping Wei and Lei Zhang

Diversity 2022, 14(8), 674; https://doi.org/10.3390/d14080674 - 18 Aug 2022

Cited by 3 | Viewed by 1516

Abstract

Land subsidence caused by underground coal mining critically influences the structure and function of ecosystems in mining areas. However, knowledge on the aquatic bacterial community structure and interspecies interactions in subsidence lakes are still limited. To address this issue, we collected water samples from a coal mining subsidence lake and its connected river and investigated the spatial distribution and co-occurrence patterns of the bacterial community using 16S rRNA amplicon sequencing. The results revealed that the bacterial α-diversity in the subsidence lake was higher than that in the river. The bacterial community composition was also significantly different between the subsidence lake and its connected river. Total nitrogen explained 21.4% of the bacterial community composition variation, while sulfate explained 38.4% of the bacterial functional composition variation. Co-occurrence network analysis indicated that the modularity indices and stability of the microbial network in the subsidence lake were significantly higher than those in rivers, which presented more resistance to environmental disturbance. Keystone bacterial taxa in the subsidence lake and river included the Clostridiaceae 1 family, and the Shewanella, Flavobacterium, and Limnohabitans genera, which play vital roles in the carbon, sulfur, and nitrogen cycles. Moreover, functional analysis showed that assimilatory sulfate reduction processes had a major role in the sulfur cycle of the subsidence lake and its connected river ecosystem. Overall, our findings provide new insights into the microbial community structure and assembly in subsidence lakes and its connected river ecosystems, with significant implications for the responsible utilization of water resources and the promotion of sustainable development in mining areas. Full article

(This article belongs to the Special Issue Diversity and Ecology of Freshwater Lake Microbial Communities)

► Show Figures

Journal Menu

Journal Browser

Diversity and Ecology of Freshwater Lake Microbial Communities

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (8 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI