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Microorganisms
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Microbial Communities in Aquatic Systems: Diversity and Function
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Microbial Communities in Aquatic Systems: Diversity and Function

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 5434

Special Issue Editor

Dr. Tamara Ivanovna Zemskaya

E-Mail Website
Guest Editor
Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
Interests: genomics of microbes in aquatic environments

Special Issue Information

Dear Colleagues,

Microorganisms are the most diverse and numerous organisms in the biosphere on our planet. At the same time, the real scale of microbial diversity, their metabolic capabilities, and environmental conditions that affect the development of certain microbial taxa and microbial communities as a whole remain largely unknown. The use of new molecular methods, coupled with traditional microbiological methods, has greatly advanced the study of microbial diversity and the determination of their evolutionary relationships and metabolic pathways. We propose to share the results of your research in the Special Issue "Microbial Communities in Aquatic Systems: Diversity and Function" and to expand our understanding of microbial communities living in different types of aquatic ecosystems, as well as to discuss the functional role of communities and individual taxa in various biotopes and to consider possible mechanisms of functioning under different environmental conditions.

We welcome research related to the diversity and to functional role of microbial communities, as well as to elucidation of their relationships with the environment in various types of aquatic ecosystems.

We look forward to reviewing your manuscripts and sharing those of the highest quality with the research community.

Dr. Tamara Ivanovna Zemskaya
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. Microorganisms 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 2700 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

  • aquatic ecosystems
  • ecological parameters (condition)
  • microbial community
  • diversity
  • metabolism
  • metagenomics
  • relationships

Published Papers (5 papers)

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Research

24 pages, 11278 KiB  
Article
A Novel View of the Diversity of Anoxygenic Phototrophic Bacteria Inhabiting the Chemocline of Meromictic Karst Lakes
by Vladimir Gorlenko, Alexander Savvichev, Vitaly Kadnikov, Igor Rusanov, Alexey Beletsky, Elena Zakharova, Nadezhda Kostrikina, Pavel Sigalevich, Elena Veslopolova and Nikolay Pimenov
Microorganisms 2024, 12(1), 13; https://doi.org/10.3390/microorganisms12010013 - 20 Dec 2023
Viewed by 889
Abstract
The rates of oxygenic and anoxygenic photosynthesis, the microorganisms responsible for these processes, and the hydrochemical characteristics of the sulfide-containing karst lakes, Black Kichier and Big Kichier (Mari El Republic), were investigated. In these lakes, a plate of anoxygenic phototrophic bacteria (APB) is [...] Read more.
The rates of oxygenic and anoxygenic photosynthesis, the microorganisms responsible for these processes, and the hydrochemical characteristics of the sulfide-containing karst lakes, Black Kichier and Big Kichier (Mari El Republic), were investigated. In these lakes, a plate of anoxygenic phototrophic bacteria (APB) is formed at the upper boundary of sulfide occurrence in the water. The phototrophic community of the chemocline zone was analyzed using a combination of high-throughput sequencing of the 16S rRNA gene fragments and light and electron microscopic techniques. Green-colored Chlorobium clathratiforme were absolutely predominant in both lakes. The minor components included green sulfur bacteria (GSB) Chlorobium spp., symbiotic consortia Chlorochromatium magnum and Pelochromatium roseum, purple sulfur bacteria (PSB) Chromatium okenii, and unidentified phylotypes of the family Chromatiaceae, as well as members of the Chloroflexota: Chloronema sp. and Oscillochloris sp. Based on the results of the molecular analysis, the taxonomic status of Ancalochloris perfilievii and other prosthecate GSB, as well as of the PSB Thiopedia rosea, which were visually revealed in the studied freshwater lakes, is discussed. Full article
(This article belongs to the Special Issue Microbial Communities in Aquatic Systems: Diversity and Function)
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14 pages, 12543 KiB  
Article
Isolation and Identification of Culturable Bacteria from South China Seawater and Preliminary Screening of Marine Biocontrol Bacteria
by Limei Guan, Hongxiu Wang, Junhui Chen, Feiying Yang, Jian Yang, Jianghuai Li and Liang Jin
Microorganisms 2023, 11(12), 2933; https://doi.org/10.3390/microorganisms11122933 - 6 Dec 2023
Viewed by 1053
Abstract
Marine microorganisms have evolved special metabolic pathways to produce numerous bioactive substances with novel structures and unique functions. This study analyzed the diversity of culturable bacteria in marine water samples from the South China Sea and screened the isolated bacteria with pathogenic fungi. [...] Read more.
Marine microorganisms have evolved special metabolic pathways to produce numerous bioactive substances with novel structures and unique functions. This study analyzed the diversity of culturable bacteria in marine water samples from the South China Sea and screened the isolated bacteria with pathogenic fungi. A total of 200 culturable strains of 72 different bacteria were obtained from 56 water samples from the South China Sea. They belonged to three phyla and four classes, namely Gammaproteobacteria, Alphaproteobacteria, Bacilli and Actinomycetia. Bacilli was the dominant class, comprising up to 59.72%, followed by Gammaproteobacteria (20.83%). Bacillus, Pseudomonas, Paenibacillus and Rhizobium were the most dominant genera. Among these strains, HY-88 and HY-91 encoding BamC, FenB and PKSI genes were selected and identified as Bacillus subtilis. The respective inhibition rates of the HY-88 caused by plate confrontation against Magnaporthe grisea, Fusarium oxysporum, Botrytis cinerea, anthrax and Botrytis cinerea were 90.91%, 54.29%, 52.17% and 51.72%, in comparison with HY-91 86.36%, 48.57%, 47.83% and 34.48%. In addition, the supernatant of HY-88 showed a lesion inhibition rate of 74.5%, which was significantly higher than HY-91 (60.55%). In addition, HY-88 and HY-91 showed strong antifungal activity to Colletotrichum viniferum on detached Shine Muscat grapes. Tolerance tests showed that the HY-88 and HY-91 grew at 10–40 °C, 7–10% NaCl and pH 3-11. HY-88 and HY-91 could inhibit various fungal plant diseases, which lays a foundation for the development of new biopesticides. Full article
(This article belongs to the Special Issue Microbial Communities in Aquatic Systems: Diversity and Function)
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11 pages, 1522 KiB  
Article
Sediment Bacteria in the Alpine Lake Sayram: Vertical Patterns in Community Composition
by Keqiang Shao, Boqiang Qin, Jianying Chao and Guang Gao
Microorganisms 2023, 11(11), 2669; https://doi.org/10.3390/microorganisms11112669 - 30 Oct 2023
Viewed by 943
Abstract
Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm [...] Read more.
Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm long sediment core from the center of Lake Sayram, the largest alpine lake in Xinjiang Uygur autonomous area, China, and used 16S rRNA gene-targeted amplicon sequencing to examine the bacterial populations. The results showed that bacterial diversity, as estimated by the Shannon index, was highest at the surface (6.9849 at 0–4 cm) and gradually decreased with depth up to 3.9983 at 68–72 cm, and then increased to 5.0927 at 96–100 cm. A total of 56 different phyla and 1204 distinct genera were observed in the sediment core of Lake Sayram. The bacterial community structure in the sediment samples from the various layers was dissimilar. The most abundant phyla in alpine Lake Sayram were Proteobacteria, Firmicutes, and Planctomycetes, accounting for 73%, 6%, and 4% of the total reads, respectively; the most abundant genera were Acinetobacter, Hydrogenophaga, and Pseudomonas, accounting for 18%, 12%, and 8% of the total reads, respectively. Furthermore, the relative abundance of Acinetobacter increased with sediment depth, while the relative abundance of Hydrogenophaga and Pseudomonas decreased with sediment depth. Our findings indicated that the nitrate-reducing bacteria (Acinetobacter, Hydrogenophaga, and Pseudomonas) may be prevalent in the sediment core of Lake Sayram. Canonical correspondence analysis showed that carbonate and total organic carbon (TOC) may be the main environmental factors affecting the vertical patterns of bacterial community composition (BCC) in the sediment of Lake Sayram. This work significantly contributes to our understanding of the BCC of sediments from alpine lakes in arid and semiarid regions. Full article
(This article belongs to the Special Issue Microbial Communities in Aquatic Systems: Diversity and Function)
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12 pages, 1887 KiB  
Article
Macromonas nakdongensis sp. nov., Isolated from Freshwater and Characterization of Bacteriophage BK-30P—The First Phage That Infects Genus Macromonas
by Kiwoon Baek and Ahyoung Choi
Microorganisms 2023, 11(9), 2237; https://doi.org/10.3390/microorganisms11092237 - 5 Sep 2023
Viewed by 790
Abstract
A Gram-stain-negative, non-motile, non-pigmented, rod-shaped bacterium was isolated from a freshwater sample of Nakdong River in South Korea and designated as strain BK-30T. An analysis of the 16S rRNA gene sequence of strain BK-30T revealed its closest phylogenetic neighbors were [...] Read more.
A Gram-stain-negative, non-motile, non-pigmented, rod-shaped bacterium was isolated from a freshwater sample of Nakdong River in South Korea and designated as strain BK-30T. An analysis of the 16S rRNA gene sequence of strain BK-30T revealed its closest phylogenetic neighbors were members of the genus Macromonas. Specifically, the strain formed a robust clade with Macromonas bipunctata DSM 12705T, sharing 98.4% similarity in their 16S rRNA gene sequences. The average nucleotide identity value between strain BK-30T and M. bipunctata DSM 12705T was 79.8%, and the genome-to-genome distance averaged 21.3%, indicating the representation of a novel genomic species. Strain BK-30T exhibited optimum growth at 30 °C and pH 7.0, in the absence of NaCl. The major respiratory isoprenoid quinone identified was ubiquinone-8 (Q-8). The principal fatty acids detected were C16:1 ω7c and/or C16:1 ω6c (49.6%), C16:0 (27.5%), and C18:1 ω7c and/or C18:1 ω6c (9.2%). The DNA G+C content of the strain was determined to be 67.3 mol%. Based on these data, we propose a novel species within the genus Macromonas, named Macromonas nakdongensis sp. nov., to accommodate the bacterial isolate. Strain BK-30T is designated as the type strain (=KCTC 52161T = JCM 31376T = FBCC-B1). Additionally, we present the isolation and complete genome sequence of a lytic phage infecting strain BK-30T, named BK-30P. This bacteriophage is the first reported to infect Macromonas, leading us to propose the name “Macromonasphage”. Full article
(This article belongs to the Special Issue Microbial Communities in Aquatic Systems: Diversity and Function)
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22 pages, 5594 KiB  
Article
Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia)
by Anna Lomakina, Sergei Bukin, Olga Shubenkova, Tatyana Pogodaeva, Vyacheslav Ivanov, Yuri Bukin and Tamara Zemskaya
Microorganisms 2023, 11(7), 1865; https://doi.org/10.3390/microorganisms11071865 - 24 Jul 2023
Cited by 1 | Viewed by 1294
Abstract
We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern [...] Read more.
We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH4 metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities. Full article
(This article belongs to the Special Issue Microbial Communities in Aquatic Systems: Diversity and Function)
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