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Abdallah RZ, Elbehery AHA, Ahmed SF, Ouf A, Malash MN, Liesack W, Siam R. Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities. mSystems 2024; 9:e0009524. [PMID: 38727215 DOI: 10.1128/msystems.00095-24] [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: 01/28/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession. IMPORTANCE Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.
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Affiliation(s)
- Rehab Z Abdallah
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Ali H A Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Shimaa F Ahmed
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Amged Ouf
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Mohamed N Malash
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, Egypt
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rania Siam
- Biology department, The American University in Cairo, Cairo, Egypt
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Li Q, Lei Y, Li T. DNA metabarcoding reveals ecological patterns and driving mechanisms of archaeal, bacterial, and eukaryotic communities in sediments of the Sansha Yongle Blue Hole. Sci Rep 2024; 14:6745. [PMID: 38509179 PMCID: PMC10954614 DOI: 10.1038/s41598-024-57214-8] [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: 08/21/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole with unique physicochemical characteristics. However, our knowledge of the biodiversity and community structure in SYBH sediments remains limited, as past studies have mostly focused on microbial communities in the water column. Here, we collected sediment samples from the aerobic zone (3.1 to 38.6 m) and the deep anaerobic zone (150 m, 300 m) of the SYBH and extracted DNA to characterize the archaeal, bacterial, and eukaryotic communities inhabiting these sediments. Our results showed that the archaeal and bacterial communities were dominated by Thaumarchaeota and Proteobacteria, respectively. The dominant taxa of eukaryotes in different sites varied greatly, mainly including Phaeophyceae, Annelida, Diatomea and Arthropoda. All three examined domains showed clear vertical distributions and significant differences in community composition between the aerobic and anaerobic zones. Sulfide played a prominent role in structuring the three domains, followed by salinity, nitrous oxide, pH, temperature and dissolved oxygen, all of which were positively correlated with the turnover component, the main contributor to beta diversity. Neutral community model revealed that stochastic processes contributed to more than half of the community variations across the three domains. Co-occurrence network showed an equal number of positive and negative interactions in the archaeal network, while positive interactions accounted for ~ 80% in the bacterial and eukaryotic networks. Our findings reveal the ecological features of prokaryotes and eukaryotes in SYBH sediments and shed new light on community dynamics and survival strategies in the special environment of marine blue holes.
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Affiliation(s)
- Qingxia Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Marine Ranching Engineering Science Research of Liaoning, Dalian Ocean University, Dalian, 116023, China
| | - Yanli Lei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tiegang Li
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
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Tapilatu Y, Fauzan I, Pradipta A, Kusuma AB. A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia. Sci Rep 2024; 14:895. [PMID: 38195681 PMCID: PMC10776683 DOI: 10.1038/s41598-024-51614-6] [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: 06/26/2023] [Accepted: 01/07/2024] [Indexed: 01/11/2024] Open
Abstract
Indonesia's deep-sea microbial communities remain poorly understood, prompting the need for comprehensive investigations. This study aimed to assess the bacterial and archaeal diversities in northwestern Arafura deep-sea sediments, spanning depths of 100 to 1,457 m using a 16S rRNA based-metagenomic sequencing approach, without technical and biological replicates. Principal component analyses based on the Bray-Curtis dissimilarity index indicated that most of the bacterial and archaeal communities were habitat-specific and influenced by depth. The most prevalent known bacterial phylotypes were detected from all samples belonging to the phylum of Desulfobacteriota, Pseudomonadota, and Firmicutes. In addition, the samples also harbored diverse members of the Archaea domain, including Crenarchaeota, Nanoarchaeota and Haloarchaeota. Notably, the sequencing data revealed the significant presence of rare prokaryotic taxa, including uncultured counterparts with less than 1% abundance. The findings suggest that novel and rare prokaryotic taxa are abundant in northwestern Arafura deep-sea ecosystem, offering unique opportunities for further bioprospecting and functional ecology studies.
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Affiliation(s)
- Yosmina Tapilatu
- Marine Microbiology and Biotechnology Laboratory, Centre for Deep-Sea Research, The National Research and Innovation Agency (PRLD BRIN), KKB Atjep Suwartana, Jl. Y. Syaranamual Guru-Guru Poka, Ambon, 97233, Indonesia.
| | - Ihsan Fauzan
- Scientific Department, Genomik Solidaritas Indonesia (GSI Lab) Inc., Jl. Sultan Agung No. 29, South Jakarta, Indonesia
| | - Ariel Pradipta
- Scientific Department, Genomik Solidaritas Indonesia (GSI Lab) Inc., Jl. Sultan Agung No. 29, South Jakarta, Indonesia
| | - Ali Budhi Kusuma
- Indonesian Centre for Extremophile Bioresources and Biotechnology, Faculty of Life Sciences and Technology, Sumbawa University of Technology (UTS), Jln. Raya Olat Maras, Desa Batu Alang, Moyo Hulu Sumbawa, 84371, Indonesia
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Qin Y, Wang N, Zheng L, Li Q, Wang L, Xu X, Yin X. Study of Archaeal Diversity in the Arctic Meltwater Lake Region. BIOLOGY 2023; 12:1023. [PMID: 37508452 PMCID: PMC10376139 DOI: 10.3390/biology12071023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/04/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023]
Abstract
Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO2--N), and nitrate nitrogen (NO3--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH4+-N, SiO32--Si, MC, NO3--N, and NO2--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.
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Affiliation(s)
- Yiling Qin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Nengfei Wang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Li Zheng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Qinxin Li
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China
| | - Long Wang
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science & Technology, Qingdao 266042, China
| | - Xiaoyu Xu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Xiaofei Yin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
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Xing G, Lu J, Xuan L, Chen J, Xiong J. Sediment prokaryotic assembly, methane cycling, and ammonia oxidation potentials in response to increasing antibiotic pollution at shrimp aquafarm. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128885. [PMID: 35421673 DOI: 10.1016/j.jhazmat.2022.128885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 05/28/2023]
Abstract
Antibiotic pollution poses serious threats to public health and ecological processes. However, systematic research regarding the interactive effects of increasing nutrient and antibiotic pollutions on the prokaryotic community, particularly taxa that contribute to greenhouse gas emissions, is lacking. By exploring the complex interactions that occur between interkingdom bacteria and archaea, biotic and abiotic factors, the responses of sediment prokaryotic assembly were determined along a significant antibiotic pollution gradient. Bacterial and archaeal communities were primarily governed by sediment antibiotic pollution, ammonia, phosphate, and redox potential, which further affected enzyme activities. The two communities nonlinearly responded to increasing antibiotic pollution, with significant tipping points of 3.906 and 0.979 mg/kg antibiotics, respectively. The combined antibiotic concentration-discriminatory taxa of bacteria and archaea accurately (98.0% accuracy) diagnosed in situ antibiotic concentrations. Co-abundance analysis revealed that the methanogens, methanotrophs, sulfate-reducing bacteria, and novel players synergistically contributed to methane cycling. Antibiotic pollution caused the dominant role of ammonia-oxidizing archaea in ammonia oxidation at these alkaline sediments. Collectively, the significant tipping points and bio-indicators afford indexes for regime shift and quantitative diagnosis of antibiotic pollution, respectively. Antibiotic pollution could expedite methane cycling and mitigate nitrous oxide yield, which are previously unrecognized ecological effects. These findings provide new insights into the interactive biological and ecological consequences of increasing nutrient and antibiotic pollutions.
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Affiliation(s)
- Guorui Xing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lixia Xuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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Zhu D, Sethupathy S, Gao L, Nawaz MZ, Zhang W, Jiang J, Sun J. Microbial diversity and community structure in deep-sea sediments of South Indian Ocean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45793-45807. [PMID: 35152353 DOI: 10.1007/s11356-022-19157-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.
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Affiliation(s)
- Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lu Gao
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Zohaib Nawaz
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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Kiama CW, Njire MM, Kambura AK, Mugweru JN, Matiru VN, Wafula EN, Kagali RN, Kuja JO. Prokaryotic diversity and composition within equatorial lakes Olbolosat and Oloiden in Kenya (Africa). CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100066. [PMID: 34841356 PMCID: PMC8610316 DOI: 10.1016/j.crmicr.2021.100066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 01/04/2023] Open
Abstract
Total community 16S rDNA was used to determine the diversity and composition of bacteria and archaea within lakes Olbolosat and Oloiden in Kenya. The V3-V4 hypervariable region of the 16S rRNA gene was targeted since it's highly conserved and has a higher resolution for lower rank taxa. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Lakes Olbolosat and Oloiden shared 280 of 10,523 Amplicon Sequence Variants (ASVs) recovered while the four sample types (water, microbial mats, dry and wet sediments) shared 4 ASVs. The composition of ASVs in lake Olbolosat was highly dependent on Cu+, Fe2+, NH4 +, and Mn2+, while L. Oloiden was dependent on Mg2+, Na+, Ca2+, and K+. All the alpha diversity indices except Simpson were highest in the dry sediment sample (EC1 and 2) both from lake Oloiden. The abundant phyla included Proteobacteria (33.8%), Firmicutes (27.3%), Actinobacteriota (21.2%), Chloroflexi (6.8%), Cyanobacteria (3.8%), Acidobacteriota (2.8%), Planctomycetota (1.9%) and Bacteroidota (1.1%). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The interaction network for prokaryotic communities within the two lakes displayed Proteobacteria to be highly positively connected with other microbes. PERMANOVA results suggest that temperature controls the functioning of the two ecosystems.
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Affiliation(s)
- Catherine Wachera Kiama
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Moses Mucugi Njire
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Anne Kelly Kambura
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300 Voi, Kenya
| | | | - Viviene Njeri Matiru
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Eliud Nalianya Wafula
- Department of Physical and Biological Sciences, Bomet University College, P.O Box 701-20400, Bomet Kenya
| | - Robert Nesta Kagali
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Josiah Ochieng Kuja
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
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Cao Q, Najnine F, Han H, Wu B, Cai J. BALOs Improved Gut Microbiota Health in Postlarval Shrimp ( Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment. Front Microbiol 2020; 11:1296. [PMID: 32714290 PMCID: PMC7344170 DOI: 10.3389/fmicb.2020.01296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.
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Affiliation(s)
- Qingqing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Farhana Najnine
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongcao Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Bing Wu
- Modern Analysis Centre, South China University of Technology, Guangzhou, China
| | - Junpeng Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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Wakung’oli M, Amoo AE, Enagbonma BJ, Babalola OO. Termite Societies Promote the Taxonomic and Functional Diversity of Archaeal Communities in Mound Soils. BIOLOGY 2020; 9:biology9060136. [PMID: 32630446 PMCID: PMC7345372 DOI: 10.3390/biology9060136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/04/2022]
Abstract
Recent studies involving microbial communities in termite mounds have been more focused on bacteria and fungi with little attention given to archaea, which play significant roles in nutrient cycling. Thus, we aimed at characterizing the archaeal taxonomic and functional diversity in two termite mound soils using the shotgun sequencing method with the assumption that termite activities could promote archaeal diversity. Our findings showed that termite mound soils have archaeal groups that are taxonomically different from their surrounding soils, with Euryarchaeota, Korarchaeota, and Nanoarchaeota being predominant while Thaumarchaeota and Crenarchaeota were predominant in the surrounding soils. Additionally, the observed nutrient pathways: phosphorus, nitrogen, and sulfur were all significantly more predominant in termite mound soils than in their comparative surrounding soils. Alpha diversity showed that archaea were not significantly different within termite mound soils and the surrounding soils. The beta diversity revealed significant differences in the archaeal taxonomic composition and their functional categories between the termite mounds and surrounding soils. Our canonical correspondence analysis revealed that the distribution of archaeal communities was likely dependent on the soil properties. Our results suggested that termite activities may promote the diversity of archaea; with some of our sequences grouped as unclassified archaea, there is a need for further research to unveil their identity.
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Behera P, Mohapatra M, Kim JY, Rastogi G. Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135709. [PMID: 31806293 DOI: 10.1016/j.scitotenv.2019.135709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated 'distance-decay' patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Ji Yoon Kim
- Center for Climate Change Adaptation, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
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