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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 18676

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Prof. Dr. Muhammad Yasir

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Guest Editor

King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
Interests: metagenomics; environmental microbial diversity; human microbiome; taxonogenomics; antibiotic resistome

Special Issue Information

Dear Colleagues,

The Earth is covered by various environments comprising diverse microbial communities that represent enormous genetic diversity. It makes life possible by managing biogeochemistry, cycling nutrients, decomposition, producing enzymes and metabolites. Generally, microbial communities are complex consortia of species that cannot be adequately studied by culture-dependent screening, as the majority of microorganisms from most environments are difficult to grow in the laboratory. Alternative means are required to achieve the true illustration of specific environment microbial communities. Advances in sequencing technologies have made genomics and metagenomics powerful tools for the deep profiling of microbial communities, and these technologies are able to answer fundamental questions in environmental microbiology. Recently, binning has made it is possible to reconstruct genomes from shotgun sequencing data generated from DNA directly extracted from the environment and thus extend the catalog of microbial genomes. Studies on microbial genomes and phenotypes have gradually moved from isolated species to environmental communities. Community genomics helps us to catch the cumulative features of a microbial population associated with a specific environment. It provides a platform to determine the community structure, genetic diversity, and metabolic potential of uncultured microorganisms and understand the dynamic interplay between microorganisms and their environment. A comparison of the sequence data within a particular environment reveals drivers that lead to genome evaluation and speciation. The gene catalog retrieved from extensive sequencing data can be exploited for biotechnology applications. The genomic analysis of environmental microbial communities will extend our knowledge of poorly studied microorganisms, enabling us to analyze their diversity, interaction with other microbes, and role in ecosystems.

For this Special Issue of Microorganisms titled "Genome Analysis of Microbial Communities in Environment", we invite you to submit both original research and review articles on any aspect related to the genomic analysis of environmental microbial communities.

Prof. Dr. Muhammad Yasir
Guest Editor

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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

environment
microbial communities
genomics
resistome
metagenomics
phylogenetic

Published Papers (9 papers)

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Research

13 pages, 2265 KiB

Open AccessArticle

Ecoinformatic Analysis of the Gut Ecological Diversity of Wild and Captive Long-Tailed Gorals Using Improved ITS2 Region Primers to Support Their Conservation

by Chang-Eon Park, Bum-Joon Cho, Min-Ji Kim, Min-Chul Kim, Min-Kyu Park, Jang-Ick Son, Hee-Cheon Park and Jae-Ho Shin

Microorganisms 2023, 11(6), 1368; https://doi.org/10.3390/microorganisms11061368 - 23 May 2023

Viewed by 977

Abstract

Ex situ conservation is used to protect endangered wildlife. As captive and wild long-tailed gorals are known to be similar, individuals under ex situ conservation can be reintroduced into nature. However, there is no appropriate indicator to evaluate them. Here, we amplified the internal transcribed spacer 2 (ITS2) region and compared the gut ecological information (eco-information) of captive and wild long-tailed gorals. We validated the existing ITS86F and ITS4 universal primers using reference sequences of the National Center for Biotechnology Information (NCBI) and improved their matching rates. We compared the gut eco-information of captive and wild long-tailed gorals obtained through experiments using the improved primer pair and found that the gut ecological diversity of captive gorals was low. Based on this, we suggested that the gut eco-information can be used as an evaluation index before reintroducing captive long-tailed gorals. Furthermore, we identified four plant types from the gut eco-information of wild long-tailed gorals, which can be the additional food sources to enhance the reduced intestinal ecological diversity of the captive animals. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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12 pages, 2315 KiB

Open AccessArticle

Antibiotic-Resistant Desulfovibrio Produces H₂S from Supplements for Animal Farming

by Olga V. Karnachuk, Alexey V. Beletsky, Andrey L. Rakitin, Olga P. Ikkert, Marat R. Avakyan, Viacheslav S. Zyusman, Andrei Napilov, Andrey V. Mardanov and Nikolai V. Ravin

Microorganisms 2023, 11(4), 838; https://doi.org/10.3390/microorganisms11040838 - 25 Mar 2023

Cited by 2 | Viewed by 2682

Abstract

Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H₂S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H₂S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H₂S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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16 pages, 4619 KiB

Open AccessArticle

Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area

by Alonso de la Garza Varela, M. Leopoldina Aguirre-Macedo and José Q. García-Maldonado

Microorganisms 2023, 11(2), 494; https://doi.org/10.3390/microorganisms11020494 - 16 Feb 2023

Viewed by 2051

Abstract

Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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16 pages, 2192 KiB

Open AccessArticle

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

by Nafi’u Abdulkadir, Joao Pedro Saraiva, Florian Schattenberg, Rodolfo Brizola Toscan, Felipe Borim Correa, Hauke Harms, Susann Müller and Ulisses Nunes da Rocha

Microorganisms 2023, 11(1), 175; https://doi.org/10.3390/microorganisms11010175 - 10 Jan 2023

Cited by 6 | Viewed by 2546

Abstract

The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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15 pages, 2892 KiB

Open AccessArticle

Genomic Investigation of Desert Streptomyces huasconensis D23 Reveals Its Environmental Adaptability and Antimicrobial Activity

by Ying Wen, Gaosen Zhang, Ali Bahadur, Yeteng Xu, Yang Liu, Mao Tian, Wei Ding, Tuo Chen, Wei Zhang and Guangxiu Liu

Microorganisms 2022, 10(12), 2408; https://doi.org/10.3390/microorganisms10122408 - 05 Dec 2022

Cited by 5 | Viewed by 2027

Abstract

The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H₂O₂). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m² (D10 = 80 J/m²) and tolerate stress up to 70 mM H₂O₂. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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17 pages, 2001 KiB

Open AccessArticle

Comparative Proteomic Analysis of an Ethyl Tert-Butyl Ether-Degrading Bacterial Consortium

by Vijayalakshmi Gunasekaran, Núria Canela and Magda Constantí

Microorganisms 2022, 10(12), 2331; https://doi.org/10.3390/microorganisms10122331 - 25 Nov 2022

Cited by 1 | Viewed by 1077

Abstract

A bacterial consortium capable of degrading ethyl tert-butyl ether (ETBE) as a sole carbon source was enriched and isolated from gasoline-contaminated water. Arthrobacter sp., Herbaspirillum sp., Pseudacidovorax sp., Pseudomonas sp., and Xanthomonas sp. were identified as the initial populations with the 16S rDNA analysis. The consortium aerobically degraded 49% of 50 mg/L of ETBE, in 6 days. The ETBE degrading efficiency of the consortium increased to 98% even with the higher concentrations of ETBE (1000 mg/L) in the subsequent subcultures, which accumulated tert-butyl alcohol (TBA). Xanthomonas sp. and Pseudomonas sp. were identified as the predominant ETBE degrading populations in the final subculture. The metaproteome of the ETBE-grown bacterial consortium was compared with the glucose-grown bacterial consortium, using 2D-DIGE. Proteins related to the ETBE metabolism, stress response, carbon metabolism and chaperones were found to be abundant in the presence of ETBE while proteins related to cell division were less abundant. The metaproteomic study revealed that the ETBE does have an effect on the metabolism of the bacterial consortium. It also enabled us to understand the responses of the complex bacterial consortium to ETBE, thus revealing interesting facts about the ETBE degrading bacterial community. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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22 pages, 4273 KiB

Open AccessArticle

Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments

by Asha Z. Goodman, Bhavya Papudeshi, Michael P. Doane, Maria Mora, Emma Kerr, Melissa Torres, Jennifer Nero Moffatt, Lais Lima, Andrew P. Nosal and Elizabeth Dinsdale

Microorganisms 2022, 10(10), 2081; https://doi.org/10.3390/microorganisms10102081 - 21 Oct 2022

Cited by 3 | Viewed by 1762

Abstract

Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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11 pages, 2472 KiB

Open AccessCommunication

Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments

by Júlia B. Gontijo, Fabiana S. Paula, Andressa M. Venturini, Jéssica A. Mandro, Paul L. E. Bodelier and Siu M. Tsai

Microorganisms 2022, 10(9), 1747; https://doi.org/10.3390/microorganisms10091747 - 30 Aug 2022

Viewed by 2137

Abstract

Although floodplains are recognized as important sources of methane (CH₄) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH₄ emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH₄ oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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11 pages, 1038 KiB

Open AccessArticle

Metagenome-Assembled Genome of Cyanocohniella sp. LLY from the Cyanosphere of Llayta, an Edible Andean Cyanobacterial Macrocolony

by Claudia Vilo, Qunfeng Dong, Alexandra Galetovic and Benito Gómez-Silva

Microorganisms 2022, 10(8), 1517; https://doi.org/10.3390/microorganisms10081517 - 27 Jul 2022

Cited by 1 | Viewed by 1862

Abstract

Cyanobacterial macrocolonies known as Llayta are found in Andean wetlands and have been consumed since pre-Columbian times in South America. Macrocolonies of filamentous cyanobacteria are niches for colonization by other microorganisms. However, the microbiome of edible Llayta has not been explored. Based on a culture-independent approach, we report the presence, identification, and metagenomic genome reconstruction of Cyanocohniella sp. LLY associated to Llayta trichomes. The assembled genome of strain LLY is now available for further inquiries and may be instrumental for taxonomic advances concerning this genus. All known members of the Cyanocohniella genus have been isolated from salty European habitats. A biogeographic gap for the Cyanocohniella genus is partially filled by the existence of strain LLY in Andes Mountains wetlands in South America as a new habitat. This is the first genome available for members of this genus. Genes involved in primary and secondary metabolism are described, providing new insights regarding the putative metabolic capabilities of Cyanocohniella sp. LLY. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)

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