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25 pages, 6699 KiB

Open AccessArticle

Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer

by Ekaterina Botchkova, Anastasia Vishnyakova, Nadezhda Popova, Marina Sukhacheva, Tatyana Kolganova, Yuriy Litti and Alexey Safonov

Biology 2023, 12(2), 221; https://doi.org/10.3390/biology12020221 - 30 Jan 2023

Cited by 3 | Viewed by 2170

Abstract

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 [...] Read more.

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N₂ at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no “conventional” nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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21 pages, 4729 KiB

Open AccessArticle

Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout

by Yang Liu, Yeteng Xu, Xiaowen Cui, Binglin Zhang, Xinyue Wang, Xiang Qin, Jinxiu Wang, Yanzhao Li, Wei Zhang, Guangxiu Liu, Tuo Chen and Gaosen Zhang

Biology 2022, 11(11), 1555; https://doi.org/10.3390/biology11111555 - 24 Oct 2022

Viewed by 1561

Abstract

Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the [...] Read more.

Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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16 pages, 3155 KiB

Open AccessArticle

Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria

by Zhenbo Lv, Jiaxin Ding, Heng Wang, Jiaxin Wan, Yifan Chen, Lewen Liang, Tiantian Yu, Yinzhao Wang and Fengping Wang

Biology 2022, 11(10), 1514; https://doi.org/10.3390/biology11101514 - 16 Oct 2022

Cited by 3 | Viewed by 2238

Abstract

Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we [...] Read more.

Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis—a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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15 pages, 3872 KiB

Open AccessArticle

Promotion of Plant Growth in Arid Zones by Selected Trichoderma spp. Strains with Adaptation Plasticity to Alkaline pH

by Juan Pablo Cabral-Miramontes, Vianey Olmedo-Monfil, María Lara-Banda, Efrén Ricardo Zúñiga-Romo and Elva Teresa Aréchiga-Carvajal

Biology 2022, 11(8), 1206; https://doi.org/10.3390/biology11081206 - 12 Aug 2022

Cited by 7 | Viewed by 1951

Abstract

Trichoderma species are filamentous fungi that support plant health and confer improved growth, disease resistance, and abiotic stress tolerance. The objective of this study is to describe the physiological characteristics of the abundance and structure of Trichoderma model strains from arid zones and [...] Read more.

Trichoderma species are filamentous fungi that support plant health and confer improved growth, disease resistance, and abiotic stress tolerance. The objective of this study is to describe the physiological characteristics of the abundance and structure of Trichoderma model strains from arid zones and evaluate and describe their possible adaptation and modulation in alkaline pH. The presence of biotic factors such as phytopathogens forces farmers to take more actions such as using pesticides. In addition, factors such as the lack of water worldwide lead to losses in agricultural production. Therefore, the search for biocontrol microorganisms that support drought opens the door to the search for variations in the molecular mechanisms involved in these phenomena. In our case, we isolated 11 tested Trichoderma fungal strains from samples collected both from the rhizosphere and roots from two endemic plants. We probed their molecular markers to obtain their identity and assessed their resistance to alkaline conditions, as well as their response to mycoparasitism, plant growth promotion, and drought stress. The findings were worthy of being analyzed in depth. Three fungal taxa/species were grouped by phylogenetic/phenotypic characteristics; three T. harzianum strains showed outstanding capabilities to adapt to alkalinity stress. They also showed antagonistic activity against three phytopathogenic fungi. Additionally, we provided evidence of significant growth promotion in Sorghum bicolor seedlings under endemic agriculture conditions and a reduction in drought damage with Trichoderma infection. Finally, beneficial fungi adapted to specific ambient niches use various molecular mechanisms to survive and modulate their metabolism. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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15 pages, 5148 KiB

Open AccessArticle

The “Infernaccio” Gorges: Microbial Diversity of Black Deposits and Isolation of Manganese-Solubilizing Bacteria

by Beatrice Farda, Rihab Djebaili, Maddalena Del Gallo, Claudia Ercole, Fabio Bellatreccia and Marika Pellegrini

Biology 2022, 11(8), 1204; https://doi.org/10.3390/biology11081204 - 11 Aug 2022

Cited by 4 | Viewed by 2192

Abstract

The present study explored the microbial diversity of black deposits found in the “Infernaccio” gorge. X-ray Powdered Diffraction (XRPD) was used to investigate the crystallinity of the samples and to identify the minerals. Scanning electron microscope and energy-dispersive X-ray spectroscopy (SEM-EDS) were used [...] Read more.

The present study explored the microbial diversity of black deposits found in the “Infernaccio” gorge. X-ray Powdered Diffraction (XRPD) was used to investigate the crystallinity of the samples and to identify the minerals. Scanning electron microscope and energy-dispersive X-ray spectroscopy (SEM-EDS) were used to detect the bacterial imprints, analyze microbe–mineral interactions, and highlight the chemical element distribution in the black deposits. 16S rRNA gene metabarcoding allowed the study of Archaea and Bacteria communities. Mn-oxide-solubilizing isolates were also obtained and characterized by culturable and molecular approaches. The multidisciplinary approach showed the occurrence of deposits composed of birnessite, diopside, halloysite, and leucite. Numerous bacterial imprints confirmed the role of microorganisms in forming these deposits. The Bacteria and Archaea communities associated with these deposits and runoff waters are dynamic and shaped by seasonal changes. The uncultured and unknown taxa are the most common and abundant. These amplicon sequence variants (ASVs) were mainly assigned to Proteobacteria and Bacteroidetes phyla. Six isolates showed interesting Mn solubilization abilities under microaerophilic conditions. Molecular characterization associated isolates to Brevibacterium, Bacillus, Neobacillus, and Rhodococcus genera. The findings enriched our knowledge of geomicrobiological aspects of one of the Earth’s hidden habitats. The study also unveiled the potential of this environment as an isolation source of biotechnologically relevant bacteria. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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24 pages, 5126 KiB

Open AccessArticle

Temperature- and Nutrients-Induced Phenotypic Changes of Antarctic Green Snow Bacteria Probed by High-Throughput FTIR Spectroscopy

by Margarita Smirnova, Valeria Tafintseva, Achim Kohler, Uladzislau Miamin and Volha Shapaval

Biology 2022, 11(6), 890; https://doi.org/10.3390/biology11060890 - 09 Jun 2022

Cited by 7 | Viewed by 2513

Abstract

Temperature fluctuations and nutrient composition are the main parameters influencing green snow microbiome. In this study we investigated the influence of temperature and nutrient conditions on the growth and cellular chemical profile of bacteria isolated from green snow. Chemical profiling of the green [...] Read more.

Temperature fluctuations and nutrient composition are the main parameters influencing green snow microbiome. In this study we investigated the influence of temperature and nutrient conditions on the growth and cellular chemical profile of bacteria isolated from green snow. Chemical profiling of the green snow bacteria was done by high-throughput FTIR spectroscopy combined with multivariate data analysis. We showed that temperature and nutrients fluctuations strongly affect growth ability and chemical profile of the green snow bacteria. The size of colonies for green snow bacteria grown at higher (25 °C) and lower (4 °C and 10 °C) than optimal temperature (18 °C) was smaller. All isolates grew on rich medium, and only 19 isolates were able to grow on synthetic minimal media. Lipid and mixed spectral regions showed to be phylogeny related. FTIR fingerprinting indicates that lipids are often affected by the temperature fluctuations. Growth on different media resulted in the change of the whole chemical profile, where lipids showed to be more affected than proteins and polysaccharides. Correlation analysis showed that nutrient composition is clearly strongly influencing chemical changes in the cells, followed by temperature. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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21 pages, 3913 KiB

Open AccessArticle

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes)

by Flavia Jaquelina Boidi, Estela Cecilia Mlewski, Guillermo César Fernández, María Regina Flores, Emmanuelle Gérard, María Eugenia Farías and Fernando Javier Gomez

Biology 2022, 11(6), 831; https://doi.org/10.3390/biology11060831 - 28 May 2022

Cited by 7 | Viewed by 4545

Abstract

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and [...] Read more.

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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17 pages, 2508 KiB

Open AccessArticle

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

by Lukas Malfertheiner, Clara Martínez-Pérez, Zihao Zhao, Gerhard J. Herndl and Federico Baltar

Biology 2022, 11(4), 599; https://doi.org/10.3390/biology11040599 - 14 Apr 2022

Cited by 6 | Viewed by 3722

Abstract

The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding [...] Read more.

The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin–Benson–Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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18 pages, 5040 KiB

Open AccessArticle

High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert

by Yang Liu, Tuo Chen, Juan Li, Minghui Wu, Guangxiu Liu, Wei Zhang, Binglin Zhang, Songlin Zhang and Gaosen Zhang

Biology 2022, 11(4), 501; https://doi.org/10.3390/biology11040501 - 24 Mar 2022

Cited by 11 | Viewed by 2374

Abstract

The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the [...] Read more.

The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m² and 6000 J/m² UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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19 pages, 2498 KiB

Open AccessArticle

Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus

by Stepan V. Toshchakov, Anna O. Izotova, Elizaveta N. Vinogradova, Gennady S. Kachmazov, Albina Y. Tuaeva, Vladimir T. Abaev, Martha A. Evteeva, Natalia M. Gunitseva, Aleksei A. Korzhenkov, Alexander G. Elcheninov, Maxim V. Patrushev and Ilya V. Kublanov

Biology 2021, 10(12), 1352; https://doi.org/10.3390/biology10121352 - 20 Dec 2021

Cited by 12 | Viewed by 3889

Abstract

The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot [...] Read more.

The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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Review

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47 pages, 1889 KiB

Open AccessReview

Biotechnology of Microorganisms from Coal Environments: From Environmental Remediation to Energy Production

by Nuraly S. Akimbekov, Ilya Digel, Kuanysh T. Tastambek, Adel K. Marat, Moldir A. Turaliyeva and Gulzhan K. Kaiyrmanova

Biology 2022, 11(9), 1306; https://doi.org/10.3390/biology11091306 - 02 Sep 2022

Cited by 11 | Viewed by 3974

Abstract

It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role [...] Read more.

It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role in coal biogeochemical dynamics and ecosystem functioning. The high oxygen content, organic fractions, and lignin-like structures of lower-rank coals may provide effective means for microbial attack, still representing a greatly unexplored frontier in microbiology. Coal degradation/conversion technology by native bacterial and fungal species has great potential in agricultural development, chemical industry production, and environmental rehabilitation. Furthermore, native microalgal species can offer a sustainable energy source and an excellent bioremediation strategy applicable to coal spill/seam waters. Additionally, the measures of the fate of the microbial community would serve as an indicator of restoration progress on post-coal-mining sites. This review puts forward a comprehensive vision of coal biodegradation and bioprocessing by microorganisms native to coal environments for determining their biotechnological potential and possible applications. Full article

(This article belongs to the Special Issue Microbial Ecology and Evolution in Extreme Environments)

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