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Chaudhary DK, Kim SE, Park HJ, Kim KH. Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp. J Microbiol Biotechnol 2024; 34:1260-1269. [PMID: 38938005 PMCID: PMC11239424 DOI: 10.4014/jmb.2403.03039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 06/29/2024]
Abstract
The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
- Division of Marine and Fisheries Life Sciences, Pukyong National University, Busan 48513, Republic of Korea
| | - Sang-Eon Kim
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
- Division of Marine and Fisheries Life Sciences, Pukyong National University, Busan 48513, Republic of Korea
| | - Hye-Jin Park
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
- Division of Marine and Fisheries Life Sciences, Pukyong National University, Busan 48513, Republic of Korea
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Li S, Xu M, Yang D, Yang M, Wu H, Li X, Yang C, Fang Z, Wu Q, Tan L, Xiao W, Weng Q. Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae. Front Microbiol 2024; 15:1400700. [PMID: 38993489 PMCID: PMC11236537 DOI: 10.3389/fmicb.2024.1400700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.
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Affiliation(s)
- Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Deying Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hejing Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuelian Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Changzhou Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan International Joint Laboratory of Virology and Immunology, Yunnan University, Kunming, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
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Wu Q, An N, Fang Z, Li S, Xiang L, Liu Q, Tan L, Weng Q. Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave. Virus Genes 2024; 60:295-308. [PMID: 38594490 PMCID: PMC11139720 DOI: 10.1007/s11262-024-02064-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.
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Affiliation(s)
- Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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Li Q, Cheng X, Liu X, Gao P, Wang H, Su C, Huang Q. Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts. Front Microbiol 2024; 15:1377721. [PMID: 38659982 PMCID: PMC11041041 DOI: 10.3389/fmicb.2024.1377721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.
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Affiliation(s)
- Qing Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Pengfei Gao
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Chuntian Su
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
| | - Qibo Huang
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
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Turrini P, Chebbi A, Riggio FP, Visca P. The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives. Front Microbiol 2024; 15:1370520. [PMID: 38572233 PMCID: PMC10987966 DOI: 10.3389/fmicb.2024.1370520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.
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Affiliation(s)
- Paolo Turrini
- Department of Science, Roma Tre University, Rome, Italy
| | - Alif Chebbi
- Department of Science, Roma Tre University, Rome, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- National Biodiversity Future Center, Palermo, Italy
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Wu Q, Yu C, Liu Y, Xing P, Li H, Li B, Wan S, Wu QL. Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China. FEMS Microbiol Ecol 2024; 100:fiad166. [PMID: 38148131 PMCID: PMC10795575 DOI: 10.1093/femsec/fiad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/17/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.
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Affiliation(s)
- Qiong Wu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyan Yu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanru Liu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- The Fuxianhu Station of Deep Lake Research, Chinese Academy of Sciences, Chengjiang 652500, China
| | - Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sino Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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Tsouggou N, Oikonomou A, Papadimitriou K, Skandamis PN. 16S and 18S rDNA Amplicon Sequencing Analysis of Aesthetically Problematic Microbial Mats on the Walls of the Petralona Cave: The Use of Essential Oils as a Cleaning Method. Microorganisms 2023; 11:2681. [PMID: 38004693 PMCID: PMC10673238 DOI: 10.3390/microorganisms11112681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems.
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Affiliation(s)
- Natalia Tsouggou
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (N.T.); (P.N.S.)
| | - Alexandra Oikonomou
- Ephorate of Palaeoanthropology and Speleology, Hellenic Republic Ministry of Culture and Sports, Ardittou 34b, 11636 Athens, Greece;
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (N.T.); (P.N.S.)
| | - Panagiotis N. Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (N.T.); (P.N.S.)
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Zhang H, Xu H, Wang S, Qin M, Zhao D, Wu QL, Zeng J. Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160418. [PMID: 36435238 DOI: 10.1016/j.scitotenv.2022.160418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.
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Affiliation(s)
- Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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11
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Cheng X, Xiang X, Yun Y, Wang W, Wang H, Bodelier PLE. Archaea and their interactions with bacteria in a karst ecosystem. Front Microbiol 2023; 14:1068595. [PMID: 36814573 PMCID: PMC9939782 DOI: 10.3389/fmicb.2023.1068595] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,College of Life Science, Shangrao Normal University, Shangrao, China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,College of Life Sciences, Nankai University, Tianjin, China
| | - Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ✉ ; ✉
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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12
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Ahamada Rachid N, Doğruöz Güngör N. Major impacts of caving activities on cave microbial diversity: case study of Morca Cave, Turkey. Int Microbiol 2022; 26:179-190. [PMID: 36331653 DOI: 10.1007/s10123-022-00287-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 06/18/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Some of microorganisms identified in cave ecosystems have been reported to play a permanent and strategic role for maintaining life of these environments. Human entrance into caves can induce some changes of cave physicochemical parameters which ultimately impacts the living organisms. In these facts, for the first time, Morca Cave was explored in a purpose to evaluate the impacts that can be caused by the human activities on microbial diversity in a limited period of time. Morca is a karts cave located in the Taşeli Plateau in the Middle Taurus mountains in Turkey. The first entrance into this cave was in 2018, and expeditors reached to - 500 m. During the second expedition in 2019, a camp was established at the - 1040-m depth during 4 days. In order to evaluate the human impacts in a new explored cave, this camping depth is chosen to be our studied area because it was its first entrance. Before the installation and at the end of the camp, sediments and surface samples were taken from different points of the camp area and around. Sequencing of 16 s rRNA of each sample to isolate DNA by using the next-generation sequencing (NGS) method was performed. The profile of the microbial diversity before the camping revealed that the class Thermoplasmata was dominated the archaea group and Gammaproteobacteria and Alphaproteobacteria were the most dominant bacterial classes. After the camp, most studied sites were noted with a decrease of microbial diversity especially the previous cited classes strains. Bacteria belonging to Bacilli class have increased after the camp. Increase of bacteria that are belonging to Bacteroidia has also observed in the most active areas. This present study highlight how cave microbial diversity can respond to the human activities within a short period inside a closed cave. Furthermore, it may constitute a solid basis and support on the improvement of techniques for cave management and expedition planning for the conservation of cave nature.
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Affiliation(s)
- Nahdhoit Ahamada Rachid
- Institute of Graduate Studies in Sciences, Istanbul University, 34134 Vezneciler Fatih, Istanbul, Turkey
| | - Nihal Doğruöz Güngör
- Department of Biology, Faculty of Science, Istanbul University, 34134 Vezneciler Fatih, Istanbul, Turkey.
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13
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Sarma S, Patel N, Patel A, Desai C, Sharma S, Dedania S, Rudakiya DM, Vishwakarma AS, Vahora S, Narra M. Rapid decomposition of rice straw by application of a novel microbial consortium and study its microbial community dynamics. World J Microbiol Biotechnol 2022; 38:212. [PMID: 36053338 DOI: 10.1007/s11274-022-03399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
Rice straw decomposition is an attractive solution to open-field burning but the traditional method has slow kinetics and takes 60-90 days to obtain mature compost. In this study, we propose to boost up the decomposition process by addition of a novel microbial consortium rich in lignocellulolytic microbes. C: N ratio of the compost reached 11.69% and degradation efficiency of cellulose and hemicellulose was found to be 64 and 87% respectively within 25 days. Lignocellulolytic activity of the microbial consortium was confirmed by plate and activity assay. These parameters clearly indicated that a mature compost was obtained in 25 days. The 16S rRNA gene amplicon sequencing and functional analysis of predicted genes indicated amino acid and carbohydrate metabolism as the major metabolic pathway during composting. The tertiary level of functional analysis revealed the major metabolic pathways in the bacterial communities as pentose phosphate pathway, glycolysis and tricarboxylic acid cycle.
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Affiliation(s)
- Shyamali Sarma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Nidhi Patel
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Aesha Patel
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Chirayu Desai
- Gujarat Biotechnology University, Near Gujarat International Finance Tec-City, Gandhinagar, Gujarat, 382355, India
| | - Shaishav Sharma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Samir Dedania
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Darshan M Rudakiya
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Alok S Vishwakarma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Samir Vahora
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Madhuri Narra
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India.
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14
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Wu F, Zhang Y, Gu JD, He D, Zhang G, Liu X, Guo Q, Cui H, Zhao J, Feng H. Community assembly, potential functions and interactions between fungi and microalgae associated with biodeterioration of sandstone at the Beishiku Temple in Northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155372. [PMID: 35489512 DOI: 10.1016/j.scitotenv.2022.155372] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Fungi, cyanobacteria and algae are specific microbial groups associated with the deterioration and safety of stone monuments. In this study, high-throughput sequencing analysis was used to investigate the diversity, distributions, ecological functions, and interaction patterns of both the fungal and microalgal (including cyanobacteria and algae) communities on sandstone in the Beishiku Temple, located on the ancient Silk Road. The results showed that the core phyla of fungi were affiliated with unclassified Lecanoromycetes, Engyodontium, Knufia, Epicoccum, Endocarpon, and Cladosporium of Ascomycota whereas the phyla of microalgae were dominated by prokaryotic Cyanobacteria and eukaryotic Chlorophyta. The environmental factors of temperature, relative humidity, and light intensity were monitored simultaneously. The structure of the microbial communities was much more strongly shaped by soluble Cl-, Na+, NO3- ions than by the light intensity, moisture content or temperature, especially for the weathered sandstone located outside the caves. The co-occurrence network analysis suggested that a more stable community structure was evident outside the caves than inside. The stronger positive connections and coexistence patterns that were detected indicate a strong adaptability of fungi and microalgae to the distinct oligotrophic microhabitats on sandstone. The metacommunity co-occurrence network exhibited the ecological predominance of fungi, and most of the functional fungi in the biofilms outside the caves belonged to the Lichenized group, based on the FUNGuild prediction. These findings highlight the ecology and functions of stone-inhabiting microorganisms to further advance the current understanding and knowledge of sandstone biodeterioration for protection and management.
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Affiliation(s)
- Fasi Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China; National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Yong Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China
| | - Dongpeng He
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China
| | - Xiaobo Liu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, Jiangsu, PR China
| | - Qinglin Guo
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Huiping Cui
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-pharm Technology Co., Ltd., Shanghai 200120, PR China
| | - Huyuan Feng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China.
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15
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Chiciudean I, Russo G, Bogdan DF, Levei EA, Faur L, Hillebrand-Voiculescu A, Moldovan OT, Banciu HL. Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments. ENVIRONMENTAL MICROBIOME 2022; 17:44. [PMID: 35978381 PMCID: PMC9386943 DOI: 10.1186/s40793-022-00438-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water. RESULTS A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities. CONCLUSIONS These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.
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Affiliation(s)
- Iulia Chiciudean
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Giancarlo Russo
- EMBL Partner Institute for Genome Editing, Life Sciences Center–Vilnius University, Vilnius, Lithuania
| | - Diana Felicia Bogdan
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Doctoral School of Integrative Biology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- National Institute for Research and Development for Optoelectronics, Research Institute for Analytical Instrumentation Subsidiary, Cluj-Napoca, Romania
| | - Luchiana Faur
- Emil Racovita Institute of Speleology, Geospeleology and Paleontology Department, Bucharest, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Alexandra Hillebrand-Voiculescu
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Biospeology and Edaphobiology Department, Emil Racovita Institute of Speleology, Bucharest, Romania
| | - Oana Teodora Moldovan
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
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16
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Favila N, Madrigal-Trejo D, Legorreta D, Sánchez-Pérez J, Espinosa-Asuar L, Eguiarte LE, Souza V. MicNet toolbox: Visualizing and unraveling a microbial network. PLoS One 2022; 17:e0259756. [PMID: 35749381 PMCID: PMC9231805 DOI: 10.1371/journal.pone.0259756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.
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Affiliation(s)
- Natalia Favila
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Legorreta
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - Jazmín Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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17
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Haidău C, Năstase-Bucur R, Bulzu P, Levei E, Cadar O, Mirea IC, Faur L, Fruth V, Atkinson I, Constantin S, Moldovan OT. A 16S rRNA Gene-Based Metabarcoding of Phosphate-Rich Deposits in Muierilor Cave, South-Western Carpathians. Front Microbiol 2022; 13:877481. [PMID: 35663904 PMCID: PMC9161362 DOI: 10.3389/fmicb.2022.877481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Muierilor Cave is one of Romania's most important show caves, with paleontological and archeological deposits. Recently, a new chamber was discovered in the cave, with unique yellow calcite crystals, fine-grained crusts, and black sediments. The deposits in this chamber were related to a leaking process from the upper level that contains fossil bones and a large pile of guano. Samples were taken from the new chamber and another passage to investigate the relationship between the substrate and microbial community. Chemical, mineralogical, and whole community 16S rRNA gene-based metabarcoding analyses were undertaken, and the base of the guano deposit was radiocarbon dated. Our study indicated bacteria linked to the presence of high phosphate concentration, most likely due to the nature of the substrate (hydroxyapatite). Bacteria involved in Fe, Mn, or N cycles were also found, as these elements are commonly identified in high concentrations in guano. Since no bat colonies or fossil bones were present in the new chamber, a high concentration of these elements could be sourced by organic deposits inside the cave (guano and fossil bones) even after hundreds of years of their deposition and in areas far from both deposits. Metabarcoding of the analyzed samples found that ∼0.7% of the identified bacteria are unknown to science, and ∼47% were not previously reported in caves or guano. Moreover, most of the identified human-related bacteria were not reported in caves or guano before, and some are known for their pathogenic potential. Therefore, continuous monitoring of air and floor microbiology should be considered in show caves with organic deposits containing bacteria that can threaten human health. The high number of unidentified taxa in a small sector of Muierilor Cave indicates the limited knowledge of the bacterial diversity in caves that can have potential applications in human health and biotechnology.
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Affiliation(s)
- Catalina Haidău
- Department of Biospeleology and Karst Edaphobiology, Emil Racovita Institute of Speleology, Bucureşti, Romania
| | - Ruxandra Năstase-Bucur
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Paul Bulzu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Erika Levei
- Research Institute for Analytical Instrumentation Subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Cluj-Napoca, Romania
| | - Oana Cadar
- Research Institute for Analytical Instrumentation Subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Cluj-Napoca, Romania
| | - Ionuţ Cornel Mirea
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
| | - Luchiana Faur
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
- Faculty of Geology and Geophysics, University of Bucharest, Bucureşti, Romania
| | - Victor Fruth
- Institute of Physical Chemistry “Ilie Murgulescu” of the Romanian Academy, Bucuresti, Romania
| | - Irina Atkinson
- Institute of Physical Chemistry “Ilie Murgulescu” of the Romanian Academy, Bucuresti, Romania
| | - Silviu Constantin
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
- Centro Nacional Sobre la Evolucion Humana, Burgos, Spain
| | - Oana Teodora Moldovan
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Centro Nacional Sobre la Evolucion Humana, Burgos, Spain
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Ai J, Guo J, Li Y, Zhong X, Lv Y, Li J, Yang A. The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities-a case study of Zhijin Cave in Southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:25858-25868. [PMID: 34854002 DOI: 10.1007/s11356-021-17783-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms, sensitive to the surrounding environment changes, show how the cave environment can be impacted by human activities. Zhijin Cave, featured with the most well-developed karst landform in China, has been open to tourists for more than 30 years. This study explored the microbial diversity in a karst cave and the impacts of tourism activities on the microbial communities and the community structures of bacteria and archaea in three niches in Zhijin Cave, including the mixture of bacteria and cyanobacteria on the rock wall, the aquatic sediments, and the surface sediments, using 16S rRNA high-throughput sequencing technology. It was found that Actinobacteriota and Proteobacteria were the dominant bacteria in the cave and Crenarchaeota and Thermoplasmatota were the dominant archaea. The correlation between microorganisms and environmental variables in the cave showed that archaea were more affected by pH and ORP than bacteria and F-, Cl-, NO3-, and SO42- were all positively relevant to the distribution of most bacteria and archaea in the cave. PICRUSt's prediction of microbial functions also indicated that abundance of the bacteria's functions was higher than that of the archaea. The intention of this study was to improve the understanding, development, and protection of microbial resources in caves.
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Affiliation(s)
- Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jianeng Guo
- Management Office of Zhijin Cave Scenic Area, Bijie, 552100, Guizhou, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xiong Zhong
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Yang Lv
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
| | - Aijiang Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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Bendia AG, Callefo F, Araújo MN, Sanchez E, Teixeira VC, Vasconcelos A, Battilani G, Pellizari VH, Rodrigues F, Galante D. Metagenome-Assembled Genomes from Monte Cristo Cave (Diamantina, Brazil) Reveal Prokaryotic Lineages As Functional Models for Life on Mars. ASTROBIOLOGY 2022; 22:293-312. [PMID: 34694925 DOI: 10.1089/ast.2021.0016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbial communities have been explored in various terrestrial subsurface ecosystems, showing metabolic potentials that could generate noteworthy morphological and molecular biosignatures. Recent advancements in bioinformatic tools have allowed for descriptions of novel and yet-to-be cultivated microbial lineages in different ecosystems due to the genome reconstruction approach from metagenomic data. Using shotgun metagenomic data, we obtained metagenome-assembled genomes related to cultivated and yet-to-be cultivated prokaryotic lineages from a silica and iron-rich cave (Monte Cristo) in Minas Gerais State, Brazil. The Monte Cristo Cave has been shown to possess a high diversity of genes involved with different biogeochemical cycles, including reductive and oxidative pathways related to carbon, sulfur, nitrogen, and iron. Three genomes were selected for pangenomic analysis, assigned as Truepera sp., Ca. Methylomirabilis sp., and Ca. Koribacter sp. based on their lifestyles (radiation resistance, anaerobic methane oxidation, and potential iron oxidation). These bacteria exhibit genes involved with multiple DNA repair strategies, starvation, and stress response. Because these groups have few reference genomes deposited in databases, our study adds important genomic information about these lineages. The combination of techniques applied in this study allowed us to unveil the potential relationships between microbial genomes and their ecological processes with the cave mineralogy and highlight the lineages involved with anaerobic methane oxidation, iron oxidation, and radiation resistance as functional models for the search for extant life-forms outside our planet in silica- and iron-rich environments and potentially on Mars.
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Affiliation(s)
- Amanda G Bendia
- Biological Oceanography Department, Oceanographic Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Flavia Callefo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Maicon N Araújo
- Fundamental Chemistry Department, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Evelyn Sanchez
- Institute of Science and Technology, Federal University of the Jequitinhonha and Mucuri, Diamantina, Brazil
| | - Verônica C Teixeira
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Alessandra Vasconcelos
- Institute of Science and Technology, Federal University of the Jequitinhonha and Mucuri, Diamantina, Brazil
| | - Gislaine Battilani
- Institute of Science and Technology, Federal University of the Jequitinhonha and Mucuri, Diamantina, Brazil
| | - Vivian H Pellizari
- Biological Oceanography Department, Oceanographic Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Rodrigues
- Fundamental Chemistry Department, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
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Benthic Biofilm Bacterial Communities and Their Linkage with Water-Soluble Organic Matter in Effluent Receivers. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19041994. [PMID: 35206183 PMCID: PMC8872271 DOI: 10.3390/ijerph19041994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023]
Abstract
Benthic biofilms are pioneering microbial aggregates responding to effluent discharge from wastewater treatment plants (WWTPs). However, knowledge of the characteristics and linkage of bacterial communities and water-soluble organic matter (WSOM) of benthic biofilms in effluent-receiving rivers remains unknown. Here, we investigated the quality of WSOM and the evolution of bacterial communities in benthic biofilm to evaluate the ecological impacts of effluent discharge on a representative receiving water. Tryptophan-like proteins showed an increased proportion in biofilms collected from the discharge area and downstream from the WWTP, especially in summer. Biofilm WSOM showed weak humic character and strong autochthonous components, and species turnover was proven to be the main factor governing biofilm bacteria community diversity patterns. The bacterial community alpha diversity, interspecies interaction, biological index, and humification index were signally altered in the biofilms from the discharge area, while the values were more similar in biofilms collected upstream and downstream from the WWTP, indicating that both biofilm bacterial communities and WSOM characters have resilience capacities. Although effluent discharge simplified the network pattern of the biofilm bacterial community, its metabolic functional abundance was basically stable. The functional abundance of carbohydrate metabolism and amino acid metabolism in the discharge area increased, and the key modules in the non-random co-occurrence network also verified the important ecological role of carbon metabolism in the effluent-receiving river. The study sheds light on how benthic biofilms respond to effluent discharge from both ecological and material points of view, providing new insights on the feasibility of utilizing benthic biofilms as robust indicators reflecting river ecological health.
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Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem. Microbiol Spectr 2021; 9:e0115221. [PMID: 34494852 PMCID: PMC8557908 DOI: 10.1128/spectrum.01152-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.
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Morse KV, Richardson DR, Brown TL, Vangundy RD, Cahoon AB. Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession. PeerJ 2021; 9:e10757. [PMID: 33732542 PMCID: PMC7950216 DOI: 10.7717/peerj.10757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave's aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave.
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Li H, Zeng J, Ren L, Yan Q, Wu QL. Enhanced Metabolic Potentials and Functional Gene Interactions of Microbial Stress Responses to a 4,100-m Elevational Increase in Freshwater Lakes. Front Microbiol 2021; 11:595967. [PMID: 33519731 PMCID: PMC7838385 DOI: 10.3389/fmicb.2020.595967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Elevation has a strong influence on microbial community composition, but its influence on microbial functional genes remains unclear in the aquatic ecosystem. In this study, the functional gene structure of microbes in two lakes at low elevation (ca. 530 m) and two lakes at high elevation (ca. 4,600 m) was examined using a comprehensive functional gene array GeoChip 5.0. Microbial functional composition, but not functional gene richness, was significantly different between the low- and high-elevation lakes. The greatest difference was that microbial communities from high-elevation lakes were enriched in functional genes of stress responses, including cold shock, oxygen limitation, osmotic stress, nitrogen limitation, phosphate limitation, glucose limitation, radiation stress, heat shock, protein stress, and sigma factor genes compared with microbial communities from the low-elevation lakes. Higher metabolic potentials were also observed in the degradation of aromatic compounds, chitin, cellulose, and hemicellulose at higher elevations. Only one phytate degradation gene and one nitrate reduction gene were enriched in the high-elevation lakes. Furthermore, the enhanced interactions and complexity among the co-occurring functional genes in microbial communities of lakes at high elevations were revealed in terms of network size, links, connectivity, and clustering coefficients, and there were more functional genes of stress responses mediating the module hub of this network. The findings of this study highlight the well-developed functional strategies utilized by aquatic microbial communities to withstand the harsh conditions at high elevations.
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Affiliation(s)
- Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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