Research

Jump to: Review

23 pages, 2434 KiB

Open AccessArticle

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

by Tatyana V. Butina, Ivan S. Petrushin, Igor V. Khanaev and Yurij S. Bukin

Microorganisms 2022, 10(2), 480; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020480 - 21 Feb 2022

Cited by 6 | Viewed by 2124

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge [...] Read more.

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

16 pages, 1894 KiB

Open AccessArticle

Coordinated Diel Gene Expression of Cyanobacteria and Their Microbiome

by Kai Wang and Xiaozhen Mou

Microorganisms 2021, 9(8), 1670; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081670 - 05 Aug 2021

Cited by 7 | Viewed by 2178

Abstract

Diel rhythms have been well recognized in cyanobacterial metabolisms. However, whether this programmed activity of cyanobacteria could elicit coordinated diel gene expressions in microorganisms (microbiome) that co-occur with cyanobacteria and how such responses in turn impact cyanobacterial metabolism are unknown. To address these [...] Read more.

Diel rhythms have been well recognized in cyanobacterial metabolisms. However, whether this programmed activity of cyanobacteria could elicit coordinated diel gene expressions in microorganisms (microbiome) that co-occur with cyanobacteria and how such responses in turn impact cyanobacterial metabolism are unknown. To address these questions, a microcosm experiment was set up using Lake Erie water to compare the metatranscriptomic variations of Microcystis cells alone, the microbiome alone, and these two together (whole water) over two day-night cycles. A total of 1205 Microcystis genes and 4779 microbiome genes exhibited significant diel expression patterns in the whole-water microcosm. However, when Microcystis and the microbiome were separated, only 515 Microcystis genes showed diel expression patterns. A significant structural change was not observed for the microbiome communities between the whole-water and microbiome microcosms. Correlation analyses further showed that diel expressions of carbon, nitrogen, phosphorous, and micronutrient (iron and vitamin B₁₂) metabolizing genes were significantly coordinated between Microcystis and the microbiome in the whole-water microcosm. Our results suggest that diel fluxes of organic carbon and vitamin B₁₂ (cobalamin) in Microcystis could cause the diel expression of microbiome genes. Meanwhile, the microbiome communities may support the growth of Microcystis by supplying them with recycled nutrients, but compete with Microcystis for iron. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

17 pages, 3402 KiB

Open AccessArticle

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

by Melanie L. Blanchette and Mark A. Lund

Microorganisms 2021, 9(6), 1207; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061207 - 03 Jun 2021

Cited by 6 | Viewed by 2797

Abstract

Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal [...] Read more.

Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

13 pages, 2284 KiB

Open AccessArticle

Extreme Weather Events Enhance DOC Consumption in a Subtropical Freshwater Ecosystem: A Multiple-Typhoon Analysis

by Chao-Chen Lai, Chia-Ying Ko, Eleanor Austria and Fuh-Kwo Shiah

Microorganisms 2021, 9(6), 1199; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061199 - 01 Jun 2021

Viewed by 2657

Abstract

Empirical evidence suggests that the frequency/intensity of extreme weather events might increase in a warming climate. It remains unclear how these events quantitatively impact dissolved organic carbon (DOC), a pool approximately equal to CO₂ in the atmosphere. This study conducted a weekly-to-biweekly [...] Read more.

Empirical evidence suggests that the frequency/intensity of extreme weather events might increase in a warming climate. It remains unclear how these events quantitatively impact dissolved organic carbon (DOC), a pool approximately equal to CO₂ in the atmosphere. This study conducted a weekly-to-biweekly sampling in a deep subtropical reservoir in the typhoon-prevailing season (June to September) from 2004 to 2009, at which 33 typhoons with distinctive precipitation (<1~362 mm d⁻¹) had passed the study site. Our analyses indicated that the phosphate (i.e., DIP; <10~181 nMP) varied positively with the intensity of the accumulated rainfall 2-weeks prior; bacteria growth rate (0.05~3.68 d⁻¹) behaved as a positive function of DIP, and DOC concentrations (54~119 µMC) changed negatively with bacterial production (1.2~26.1 mgC m⁻³ d⁻¹). These implied that the elevated DIP-loading in the hyperpycnal flow induced by typhoons could fuel bacteria growth and cause a significant decline of DOC concentrations. As the typhoon’s intensity increases, many mineral-limited lentic freshwater ecosystems might become more like a CO₂ source injecting more CO₂ back to the atmosphere, creating a positive feedback loop that might generate severer extreme weather events. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

21 pages, 2826 KiB

Open AccessArticle

Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal

by Agnia Dmitrievna Galachyants, Andrey Yurjevich Krasnopeev, Galina Vladimirovna Podlesnaya, Sergey Anatoljevich Potapov, Elena Viktorovna Sukhanova, Irina Vasiljevna Tikhonova, Ekaterina Andreevna Zimens, Marsel Rasimovich Kabilov, Natalia Albertovna Zhuchenko, Anna Sergeevna Gorshkova, Maria Yurjevna Suslova and Olga Ivanovna Belykh

Microorganisms 2021, 9(4), 842; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040842 - 14 Apr 2021

Cited by 7 | Viewed by 2606

Abstract

The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing [...] Read more.

The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

31 pages, 5841 KiB

Open AccessArticle

Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

by Tatyana V. Butina, Yurij S. Bukin, Ivan S. Petrushin, Alexey E. Tupikin, Marsel R. Kabilov and Sergey I. Belikov

Microorganisms 2021, 9(4), 760; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040760 - 05 Apr 2021

Cited by 13 | Viewed by 3217

Abstract

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples [...] Read more.

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

20 pages, 2799 KiB

Open AccessArticle

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network

by Dominik Forster, Zhishuai Qu, Gianna Pitsch, Estelle P. Bruni, Barbara Kammerlander, Thomas Pröschold, Bettina Sonntag, Thomas Posch and Thorsten Stoeck

Microorganisms 2021, 9(3), 549; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030549 - 06 Mar 2021

Cited by 17 | Viewed by 3295

Abstract

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, [...] Read more.

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Water temperature belonged to the strongest environmental parameters splitting the data into two distinct seasonal networks (October–April; May–September). The expected ecological niche of phytoplankton, weakened through nutrient depletion because of permanent thermal stratification and through parasitic fungi, was occupied by the cyanobacterium Planktothrix rubescens and mixotrophic nanoflagellates. Instead of phytoplankton, bacteria and nanoflagellates were the main prey organisms associated with key predators (ciliates), which contrasts traditional views of biological associations in lake plankton. In a species extinction scenario, the warm season network emerged as more vulnerable than the cold season network, indicating a time-lagged effect of warmer winter temperatures on the communities. We conclude that climate stressors compromise lake ecosystem robustness and resilience through species replacement, richness differences, and succession as indicated by key network properties. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

Review

Jump to: Research

17 pages, 3577 KiB

Open AccessReview

Phylum Gemmatimonadota and Its Role in the Environment

by Izabela Mujakić, Kasia Piwosz and Michal Koblížek

Microorganisms 2022, 10(1), 151; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010151 - 12 Jan 2022

Cited by 68 | Viewed by 4952

Abstract

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. [...] Read more.

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments

Share This Special Issue

Special Issue Editors

Special Issue Information

Published Papers (8 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI