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Liu T, Lee S, Kim M, Fan P, Boughton RK, Boucher C, Jeong KC. A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134694. [PMID: 38788585 DOI: 10.1016/j.jhazmat.2024.134694] [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: 01/20/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.
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Affiliation(s)
- Ting Liu
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA; Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Shinyoung Lee
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA; Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Miju Kim
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA; Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611 USA; Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Peixin Fan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA; Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Raoul K Boughton
- Range Cattle Research and Education Center, Wildlife Ecology and Conservation, University of Florida, Ona, FL 33865, USA
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611 USA
| | - Kwangcheol C Jeong
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA; Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611 USA.
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Rout AK, Dixit S, Tripathy PS, Rout SS, Parida SN, Parida PK, Sarkar DJ, Kumar Das B, Singh AK, Behera BK. Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134377. [PMID: 38663298 DOI: 10.1016/j.jhazmat.2024.134377] [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: 12/25/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024]
Abstract
The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar 751003, India
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Sushree Swati Rout
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Satya Narayan Parida
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Ashok Kumar Singh
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India.
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Santos MVA, Morais JC, Veras STS, Leite WRM, Florencio L, Kato MT. Partial nitrification and simultaneous denitrification in sequential anaerobic and aerobic reactors: performance and microbial community dynamics. ENVIRONMENTAL TECHNOLOGY 2024:1-14. [PMID: 38830114 DOI: 10.1080/09593330.2024.2361930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
ABSTRACTThe removal of organic matter and nitrogen from domestic sewage was evaluated using a system composed of two sequential reactors: an anaerobic reactor (ANR) with suspended sludge and an aerobic (AER) reactor with suspended and adhered sludge to polyurethane foams. Nitrogen removal consisted of AER operating at low dissolved oxygen (DO) concentrations; this favoured the simultaneous nitrification and denitrification (SND) process. The concentration of COD and N were 440 mgO2.L-1 and 37 mgTN.L-1, respectively. The operation was divided into three phases (P), lasting 51, 53, and 46 days, respectively. The initial DO concentrations applied in the AER were: 3.0 (PI) and 1.5 mg.L-1 (PII and PIII). In PIII, the AER effluent was recirculated to the ANR at a ratio of 0.25. Kinetic assays were performed to determine the nitrification and denitrification rates of the biomasses (ANR and AER in PIII). Changes in the microbial community were evaluated throughout phases PI to PIII by massive sequencing. In PIII, the best results obtained for chemical oxygen demand (COD) and total nitrogen (TN-N) removal efficiencies, were close to 94% and 65%, respectively. Under these conditions, system effluent concentrations below 30 mg COD.L-1 and 15 mg TN-N.L-1 were verified. The nitritation and nitration rates were 10.5 and 6.5 mg N.g VSS-1.h-1, while the denitrification via nitrite and nitrate were 6.8 and 5.8 mg N.g VSS-1.h-1, respectively. A mixotrophic community was prevalent, with Rhodococcus, Nitrosomonas, Pseudomnas, and Porphyromonas being dominant or co-dominant in most of the samples, confirming the SND process in the AER sludge.
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Affiliation(s)
- Marcus V A Santos
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Juliana C Morais
- Department of Infrastructure and Civil Construction, Federal Institute of Pernambuco, Recife, Brazil
| | - Shyrlane T S Veras
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Wanderli R M Leite
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Lourdinha Florencio
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
| | - Mario T Kato
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, Brazil
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Babalola OO, Adedayo AA, Akinola SA. High-throughput metagenomic assessment of Cango Cave microbiome-A South African limestone cave. Data Brief 2024; 54:110381. [PMID: 38665155 PMCID: PMC11043842 DOI: 10.1016/j.dib.2024.110381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms inhabiting caves exhibit medical or biotechnological promise, most of which have been attributed to factors such as antimicrobial activity or the induction of mineral precipitation. This dataset explored the shotgun metagenomic sequencing of the Cango cave microbial community in Oudtshoorn, South Africa. The aimed to elucidate both the structure and function of the microbial community linked to the cave. DNA sequencing was conducted using the Illumina NovaSeq platform, a next-generation sequencing. The data comprises 4,738,604 sequences, with a cumulative size of 1,180,744,252 base pairs and a GC content of 52%. Data derived from the metagenome sequences can be accessed through the bioproject number PRJNA982691 on NCBI. Using an online metagenome server, MG-RAST, the subsystem database revealed that bacteria displayed the highest taxonomical representation, constituting about 98.66%. Archaea accounted for 0.05%, Eukaryotes at 1.20%, viruses were 0.07%, while unclassified sequences had a representation of 0.02%. The most abundant phyla were Proteobacteria (81.74%), Bacteroidetes (10.57%), Actinobacteria (4.16%), Firmicutes (SK‒1.03%), Acidobacteria (0.20), and Planctomycetes (SK‒0.16%). Functional annotation using subsystem analysis revealed that clustering based on subsystems had 13.44%, while amino acids and derivatives comprised 11.41%. Carbohydrates sequences constituted 9.55%, along with other advantageous functional traits essential for growth promotion and plant management.
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Affiliation(s)
- Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South Africa
| | - Afeez Adesina Adedayo
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South Africa
| | - Saheed Adekunle Akinola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South Africa
- Department of Microbiology and Parasitology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [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: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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Alsharif SM, Ismaeil M, Saeed AM, El-Sayed WS. Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment. BMC Microbiol 2024; 24:176. [PMID: 38778276 PMCID: PMC11110206 DOI: 10.1186/s12866-024-03291-8] [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: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants. MATERIALS AND METHODS The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes. RESULTS Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments. CONCLUSION This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.
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Affiliation(s)
- Sultan M Alsharif
- Department of Biology, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Mohamed Ismaeil
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | - Ali M Saeed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Wael S El-Sayed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
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Ali A, Vishnivetskaya TA, Chauhan A. Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches. Braz J Microbiol 2024:10.1007/s42770-024-01365-3. [PMID: 38758507 DOI: 10.1007/s42770-024-01365-3] [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: 03/09/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.
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Affiliation(s)
- Ahmad Ali
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India
| | | | - Archana Chauhan
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India.
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Barno AR, Green K, Rohwer F, Silveira CB. Snow viruses and their implications on red snow algal blooms. mSystems 2024; 9:e0008324. [PMID: 38647296 PMCID: PMC11097641 DOI: 10.1128/msystems.00083-24] [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: 01/24/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024] Open
Abstract
Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We hypothesize that these algal blooms affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of double-stranded DNA virus communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Putative snow viruses encoded genes involved in energy metabolisms, such as NAD+ synthesis and salvage pathways. In model phages, these genes facilitate increased viral particle production and lysis rates. The frequency of temperate phages was positively correlated with microbial abundance in the snow samples. These results suggest the increased frequency of temperate virus-bacteria interactions as microbial densities increase during snowmelt. We propose that this virus-bacteria dynamic may facilitate the red snow algae growth stimulated by bacteria.IMPORTANCEMicrobial communities in red snow algal blooms contribute to intensifying snowmelt rates. The role of viruses in snow during this environmental shift, however, has yet to be elucidated. Here, we characterize novel viruses extracted from snow viral metagenomes and define the functional capacities of snow viruses in both white and red snow. These results are contextualized using the composition and functions observed in the bacterial communities from the same snow samples. Together, these data demonstrate the energy metabolism performed by viruses and bacteria in a snow algal bloom, as well as expand the overall knowledge of viral genomes in extreme environments.
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Affiliation(s)
- Adam R. Barno
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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Corrêa PS, Fernandes MA, Jimenez CR, Mendes LW, Lima PDMT, Abdalla AL, Louvandini H. Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs. FEMS Microbiol Ecol 2024; 100:fiae083. [PMID: 38821514 PMCID: PMC11165275 DOI: 10.1093/femsec/fiae083] [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: 07/28/2023] [Revised: 03/21/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Murilo Antonio Fernandes
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Paulo de Mello Tavares Lima
- Department of Animal Science, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, United States
| | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
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Bombaywala S, Bajaj A, Dafale NA. Meta-analysis of wastewater microbiome for antibiotic resistance profiling. J Microbiol Methods 2024; 223:106953. [PMID: 38754482 DOI: 10.1016/j.mimet.2024.106953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
The microbial composition and stress molecules are main drivers influencing the development and spread of antibiotic resistance bacteria (ARBs) and genes (ARGs) in the environment. A reliable and rapid method for identifying associations between microbiome composition and resistome remains challenging. In the present study, secondary metagenome data of sewage and hospital wastewaters were assessed for differential taxonomic and ARG profiling. Subsequently, Random Forest (RF)-based ML models were used to predict ARG profiles based on taxonomic composition and model validation on hospital wastewaters. Total ARG abundance was significantly higher in hospital wastewaters (15 ppm) than sewage (5 ppm), while the resistance towards methicillin, carbapenem, and fluoroquinolone were predominant. Although, Pseudomonas constituted major fraction, Streptomyces, Enterobacter, and Klebsiella were characteristic of hospital wastewaters. Prediction modeling showed that the relative abundance of pathogenic genera Escherichia, Vibrio, and Pseudomonas contributed most towards variations in total ARG count. Moreover, the model was able to identify host-specific patterns for contributing taxa and related ARGs with >90% accuracy in predicting the ARG subtype abundance. More than >80% accuracy was obtained for hospital wastewaters, demonstrating that the model can be validly extrapolated to different types of wastewater systems. Findings from the study showed that the ML approach could identify ARG profile based on bacterial composition including 16S rDNA amplicon data, and can serve as a viable alternative to metagenomic binning for identification of potential hosts of ARGs. Overall, this study demonstrates the promising application of ML techniques for predicting the spread of ARGs and provides guidance for early warning of ARBs emergence.
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Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhay Bajaj
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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11
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Cai H, McLimans CJ, Jiang H, Chen F, Krumholz LR, Hambright KD. Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes. MICROBIOME 2024; 12:88. [PMID: 38741135 PMCID: PMC11089705 DOI: 10.1186/s40168-024-01801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates. RESULTS During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria. CONCLUSIONS Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.
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Affiliation(s)
- Haiyuan Cai
- School of Biological Sciences, University of Oklahoma, Norman, USA
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | | | - Helong Jiang
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, USA
| | - Lee R Krumholz
- School of Biological Sciences, University of Oklahoma, Norman, USA
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12
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Chen K, Litfin T, Singh J, Zhan J, Zhou Y. MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae018. [PMID: 38872612 DOI: 10.1093/gpbjnl/qzae018] [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: 02/14/2023] [Revised: 09/24/2023] [Accepted: 10/31/2023] [Indexed: 06/15/2024]
Abstract
Recent success of AlphaFold2 in protein structure prediction relied heavily on co-evolutionary information derived from homologous protein sequences found in the huge, integrated database of protein sequences (Big Fantastic Database). In contrast, the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search. Here, we built a comprehensive database by incorporating the non-coding RNA (ncRNA) sequences from RNAcentral, the transcriptome assembly and metagenome assembly from metagenomics RAST (MG-RAST), the genomic sequences from Genome Warehouse (GWH), and the genomic sequences from MGnify, in addition to the nucleotide (nt) database and its subsets in National Center of Biotechnology Information (NCBI). The resulting Master database of All possible RNA sequences (MARS) is 20-fold larger than NCBI's nt database or 60-fold larger than RNAcentral. The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques. It also yields more accurate and more sensitive multiple sequence alignments (MSAs) than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam. The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs. MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037, and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.
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Affiliation(s)
- Ke Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
- Peking University Shenzhen Graduate School, Shenzhen 518055, China
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Jaswinder Singh
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Jian Zhan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yaoqi Zhou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
- Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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13
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Hancock TL, Dahedl EK, Kratz MA, Urakawa H. The synchronicity of bloom-forming cyanobacteria transcription patterns and hydrogen peroxide dynamics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123812. [PMID: 38527584 DOI: 10.1016/j.envpol.2024.123812] [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: 10/04/2023] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Hydrogen peroxide is a reactive oxygen species (ROS) naturally occurring at low levels in aquatic environments and production varies widely across different ecosystems. Oxygenic photosynthesis generates hydrogen peroxide as a byproduct, of which some portion can be released to ambient water. However, few studies have examined hydrogen peroxide dynamics in relation to cyanobacterial harmful algal blooms (cHABs). A year-long investigation of algal succession and hydrogen peroxide dynamics was conducted at the Caloosahatchee River, Florida, USA. We aimed to identify potential biological mechanisms responsible for elevated hydrogen peroxide production during cHAB events through the exploration of the freshwater microbial metatranscriptome. Hydrogen peroxide concentrations were elevated from February to September of 2021 when cyanobacteria were active and abundant. We observed one Microcystis cHAB event in spring and one in winter. Both had distinct nutrient uptake and cyanotoxin gene expression patterns. While meaningful levels of microcystin were only detected during periods of elevated hydrogen peroxide, cyanopeptolin was by far the most expressed cyanotoxin during the spring bloom when hydrogen peroxide was at its yearly maxima. Gene expressions of five microbial enzymes (Rubisco, superoxide dismutase, cytochrome b559, pyruvate oxidase, and NADH dehydrogenase) positively correlated to hydrogen peroxide concentrations. Additionally, there was higher nitrogen-fixing gene (nifDKH) expression by filamentous cyanobacteria after the spring bloom but no secondary bloom formation occurred. Overall, elevated environmental hydrogen peroxide concentrations were linked to cyanobacterial dominance and greater expression of specific enzymes in the photosynthesis of cyanobacteria. This implicates cyanobacterial photosynthesis and growth results in increased hydrogen peroxide generation as reflected in measured environmental concentrations.
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Affiliation(s)
- Taylor L Hancock
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Elizabeth K Dahedl
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Michael A Kratz
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Hidetoshi Urakawa
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA.
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Vilela C, Araújo B, Soares-Guedes C, Caridade-Silva R, Martins-Macedo J, Teixeira C, Gomes ED, Prudêncio C, Vieira M, Teixeira FG. From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson's Disease Treatment? Cells 2024; 13:770. [PMID: 38727306 PMCID: PMC11083070 DOI: 10.3390/cells13090770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) is recognized as the second most prevalent primary chronic neurodegenerative disorder of the central nervous system. Clinically, PD is characterized as a movement disorder, exhibiting an incidence and mortality rate that is increasing faster than any other neurological condition. In recent years, there has been a growing interest concerning the role of the gut microbiota in the etiology and pathophysiology of PD. The establishment of a brain-gut microbiota axis is now real, with evidence denoting a bidirectional communication between the brain and the gut microbiota through metabolic, immune, neuronal, and endocrine mechanisms and pathways. Among these, the vagus nerve represents the most direct form of communication between the brain and the gut. Given the potential interactions between bacteria and drugs, it has been observed that the therapies for PD can have an impact on the composition of the microbiota. Therefore, in the scope of the present review, we will discuss the current understanding of gut microbiota on PD and whether this may be a new paradigm for treating this devastating disease.
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Affiliation(s)
- Cristiana Vilela
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Bruna Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Carla Soares-Guedes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Rita Caridade-Silva
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Joana Martins-Macedo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Catarina Teixeira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Eduardo D. Gomes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Cristina Prudêncio
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Mónica Vieira
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Fábio G. Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
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15
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Omar KM, Kitundu GL, Jimoh AO, Namikelwa DN, Lisso FM, Babajide AA, Olufemi SE, Awe OI. Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ 2024; 12:e17181. [PMID: 38666081 PMCID: PMC11044882 DOI: 10.7717/peerj.17181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
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Affiliation(s)
- Kauthar M. Omar
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - George L. Kitundu
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Adijat O. Jimoh
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Dorcus N. Namikelwa
- Department of Data Management, Modelling and Geo-Information Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Felix M. Lisso
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Abiola A. Babajide
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Seun E. Olufemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Olaitan I. Awe
- African Society for Bioinformatics and Computational Biology, Cape Town, South Africa
- Department of Computer Science, University of Ibadan, Ibadan, Oyo State, Nigeria
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16
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Jenkins JA, Draugelis-Dale RO, Hoffpauir NM, Baudoin BA, Matkin C, Driver L, Hodges S, Brown BL. Flow cytometric assessments of metabolic activity in bacterial assemblages provide insight into ecosystem condition along the Buffalo National River, Arkansas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170462. [PMID: 38311076 DOI: 10.1016/j.scitotenv.2024.170462] [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: 08/29/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024]
Abstract
The Buffalo National River (BNR), on karst terrain in Arkansas, is considered an extraordinary water resource. Water collected in Spring 2017 along BNR was metagenomically analyzed using 16S rDNA, and for 17 months (5/2017-11/2018), bacterial responses were measured in relation to nutrients sampled along a stretch of BNR near a concentrated animal feed operation (CAFO) on Big Creek. Because cell count and esterase activity can increase proportionally with organic enrichment, they were hypothesized to be elevated near the CAFO. Counts (colony forming units; CFUs) were different among sites for 73 % of the months; Big Creek generated highest CFUs 27 % of the time, with the closest downstream site at 13.3 %. Esterase activity was different among sites 94 % of the time, with Big Creek exhibiting lowest activity 71 % of the time. Over the months, activity was similar across sites at ~70 % active, except at Big Creek (56 %). The α-diversity of BNR microbial consortia near a wastewater treatment plant (WWTP) and the CAFO was related to distance from the WWTP and CAFO. The inverse relationship between high CFUs and low esterase activity at Big Creek (r = -0.71) actuated in vitro exposures of bacteria to organic wastewater contaminants (OWC) previously identified in the watershed. Exponential-phase Escherichia coli (stock strain), Streptococcus suis (avirulent, from swine), and S. dysgalactiae (virulent, from silver carp, Hypophthalmichthys molitrix) were incubated with atrazine, pharmaceuticals (17 α-ethynylestradiol and trenbolone), and antimicrobials (tylosin and butylparaben). Bacteria were differentially responsive. Activity varied with exposure time and OWC type, but not concentration; atrazine decreased it most. Taken together - the metagenomic taxonomic similarities along BNR, slightly higher bacterial growth and lower bacterial esterase at the CAFO, and the lab exposures of bacterial strains showing that OWC altered metabolism - the results indicated that bioactive OWC entering the watershed can strongly influence microbial processes in the aquatic ecosystem.
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Affiliation(s)
- Jill A Jenkins
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA 70506, USA.
| | - Rassa O Draugelis-Dale
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA 70506, USA
| | - Nina M Hoffpauir
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA 70506, USA
| | - Brooke A Baudoin
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA 70506, USA
| | - Caroline Matkin
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA 70506, USA.
| | - Lucas Driver
- U.S. Geological Survey, Lower Mississippi-Gulf Water Science Center, 401 Hardin Rd., Little Rock, AR 72211, USA.
| | - Shawn Hodges
- Buffalo National River, National Park Service, 402 N. Walnut St., Harrison, AR 72601, USA.
| | - Bonnie L Brown
- Department of Biological Sciences, University of New Hampshire, 105 Main St., Durham, NH 03824, USA.
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17
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Costa JL, Silva LG, Veras STS, Gavazza S, Florencio L, Motteran F, Kato MT. Use of nitrate, sulphate, and iron (III) as electron acceptors to improve the anaerobic degradation of linear alkylbenzene sulfonate: effects on removal potential and microbiota diversification. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33158-4. [PMID: 38613756 DOI: 10.1007/s11356-024-33158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/27/2024] [Indexed: 04/15/2024]
Abstract
Linear alkylbenzene sulfonate (LAS) is a synthetic anionic surfactant that is found in certain amounts in wastewaters and even in water bodies, despite its known biodegradability. This study aimed to assess the influence of nitrate, sulphate, and iron (III) on LAS anaerobic degradation and biomass microbial diversity. Batch reactors were inoculated with anaerobic biomass, nutrients, LAS (20 mg L-1), one of the three electron acceptors, and ethanol (40 mg L-1) as a co-substrate. The control treatments, with and without co-substrate, showed limited LAS biodegradation efficiencies of 10 ± 2% and 0%, respectively. However, when nitrate and iron (III) were present without co-substrate, biodegradation efficiencies of 53 ± 4% and 75 ± 3% were achieved, respectively, which were the highest levels observed. Clostridium spp. was prominent in all treatments, while Alkaliphilus spp. and Bacillus spp. thrived in the presence of iron, which had the most significant effect on LAS biodegradation. Those microorganisms were identified as crucial in affecting the LAS anaerobic degradation. The experiments revealed that the presence of electron acceptors fostered the development of a more specialised microbiota, especially those involved in the LAS biodegradation. A mutual interaction between the processes of degradation and adsorption was also shown.
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Affiliation(s)
- Joelithon L Costa
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Luiz Galdino Silva
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Shyrlane T S Veras
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Sávia Gavazza
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Lourdinha Florencio
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Fabrício Motteran
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil
| | - Mario Takayuki Kato
- Department of Civil and Environmental Engineering, Laboratory of Environmental Sanitation, Federal University of Pernambuco, Recife, PE, Brazil.
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Fagunwa O, Davies K, Bradbury J. The Human Gut and Dietary Salt: The Bacteroides/ Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond. Nutrients 2024; 16:942. [PMID: 38612976 PMCID: PMC11013828 DOI: 10.3390/nu16070942] [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: 01/23/2024] [Revised: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.
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Affiliation(s)
- Omololu Fagunwa
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
| | - Kirsty Davies
- School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK;
| | - Jane Bradbury
- School of Medicine, Edge Hill University, Ormskirk L39 4QP, UK;
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Zhai T, Ren W, Ji X, Wang Y, Chen H, Jin Y, Liang Q, Zhang N, Huang J. Distinct compositions and functions of circulating microbial DNA in the peripheral blood compared to fecal microbial DNA in healthy individuals. mSystems 2024; 9:e0000824. [PMID: 38426796 PMCID: PMC10949464 DOI: 10.1128/msystems.00008-24] [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: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
The crucial function of circulating microbial DNA (cmDNA) in peripheral blood is gaining recognition because of its importance in normal physiology and immunity in healthy individuals. Evidence suggests that cmDNA in peripheral blood is derived from highly abundant, translocating gut microbes. However, the associations with and differences between cmDNA in peripheral blood and the gut microbiome remain unclear. We collected blood, urine, and fecal samples from volunteers to compare their microbial information via 16S rDNA sequencing. The results revealed that, compared with gut microbial DNA, cmDNA in peripheral blood was associated with reduced diversity and a distinct microbiota composition. The cmDNA in the blood reflects the biochemical processes of microorganisms, including synthesis, energy conversion, degradation, and adaptability, surpassing that of fecal samples. Interestingly, cmDNA in blood showed a limited presence of DNA from anaerobes and gram-positive bacteria, which contrast with the trend observed in fecal samples. Furthermore, analysis of cmDNA revealed traits associated with mobile elements and potential pathologies, among others, which were minimal in stool samples. Notably, cmDNA analysis indicated similarities between the microbial functions and phenotypes in blood and urine samples, although greater diversity was observed in urine samples. Source Tracker analysis suggests that gut microbes might not be the main source of blood cmDNA, or a selective mechanism allows only certain microbial DNA into the bloodstream. In conclusion, our study highlights the composition and potential functions associated with cmDNA in peripheral blood, emphasizing its selective presence; however, further research is required to elucidate the mechanisms involved.IMPORTANCEOur research provides novel insights into the unique characteristics and potential functional implications of circulating microbial DNA (cmDNA) in peripheral blood. Unlike other studies that analyzed sequencing data from fecal or blood microbiota in different study cohorts, our comparative analysis of cmDNA from blood, urine, and fecal samples from the same group of volunteers revealed a distinct blood-specific cmDNA composition. We discovered a decreased diversity of microbial DNA in blood samples compared to fecal samples as well as an increased presence of biochemical processes microbial DNA in blood. Notably, we add to the existing knowledge by documenting a reduced abundance of anaerobes and gram-positive bacteria in blood compared to fecal samples according to the analysis of cmDNA and gut microbial DNA, respectively. This observation suggested that a potential selective barrier or screening mechanism might filter microbial DNA molecules, indicating potential selectivity in the translocation process which contrasts with the traditional view that cmDNA primarily originates from random translocation from the gut and other regions. By highlighting these differences, our findings prompt a reconsideration of the origin and role of cmDNA in blood circulation and suggest that selective processes involving more complex biological mechanisms may be involved.
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Affiliation(s)
- Taiyu Zhai
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Wenbo Ren
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Xufeng Ji
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Yifei Wang
- College of Medical Technology, Beihua University, Jilin, China
| | - Haizhen Chen
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Yuting Jin
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Qiao Liang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Nan Zhang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
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20
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Hancock TL, Dahedl EK, Kratz MA, Urakawa H. Synechococcus dominance induced after hydrogen peroxide treatment of Microcystis bloom in the Caloosahatchee River, Florida. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123508. [PMID: 38325511 DOI: 10.1016/j.envpol.2024.123508] [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: 12/22/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Few field trials examining hydrogen peroxide as a cyanobacterial harmful algal bloom (cHAB) treatment have been conducted in subtropical and tropical regions. None have been tested in Florida, home to Lake Okeechobee and downstream waterways which periodically experience Microcystis bloom events. To investigate treatment effects in Florida, we applied a 490 μM (16.7 mg/L; 0.0015%) hydrogen peroxide spray to a minor bloom of Microcystis aeruginosa on the downstream side of Franklin Lock and Dam in the Caloosahatchee River. Although hydrogen peroxide decreased to background level one day post-treatment, succession was observed in phytoplankton community amplicon sequencing. The relative abundance of Microcystis decreased on day 3 by 86%, whereas the picocyanobacteria Synechococcus became dominant, increasing by 77% on day 3 and by 173% on day 14 to 57% of the phytoplankton community. Metatranscriptomics revealed Synechococcus likely benefitted from the antioxidant defense of upregulated peroxiredoxin, peroxidase/catalase, and rubrerythrin expressions immediately after treatment, and upregulated nitrate transport and urease to take advantage of available nitrogen. Our results indicated hydrogen peroxide induces succession of the phytoplankton community from Microcystis to non-toxic picocyanobacteria and could be used for selective suppression of harmful cyanobacteria.
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Affiliation(s)
- Taylor L Hancock
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Elizabeth K Dahedl
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Michael A Kratz
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Hidetoshi Urakawa
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA.
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21
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Doloman A, de Bruin S, van Loosdrecht MCM, Sousa DZ, Lin Y. Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges. WATER RESEARCH 2024; 252:121240. [PMID: 38330717 DOI: 10.1016/j.watres.2024.121240] [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: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30-50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.
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Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, the Netherlands.
| | | | - Mark C M van Loosdrecht
- Department of Biotechnology, TU Delft, the Netherlands; Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Denmark
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, the Netherlands; Centre for Living Technologies, EWUU Alliance, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, TU Delft, the Netherlands
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22
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Hancock TL, Dahedl EK, Kratz MA, Urakawa H. Bacterial community shifts induced by high concentration hydrogen peroxide treatment of Microcystis bloom in a mesocosm study. HARMFUL ALGAE 2024; 133:102587. [PMID: 38485437 DOI: 10.1016/j.hal.2024.102587] [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: 09/11/2023] [Revised: 12/18/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
Hydrogen peroxide has gained popularity as an environmentally friendly treatment for cyanobacterial harmful algal blooms (cHABs) that takes advantage of oxidative stress sensitivity in cyanobacteria at controlled concentrations. Higher concentrations of hydrogen peroxide treatments may seem appealing for more severe cHABs but there is currently little understanding of the environmental impacts of this approach. Of specific concern is the associated microbial community, which may play key roles in the succession/recovery process post-treatment. To better understand impacts of a high concentration treatment on non-target microbial communities, we applied a hydrogen peroxide spray equating to a total volume concentration of 14 mM (473 mg/L, 0.04%) to 250 L mesocosms containing Microcystis bloom biomass, monitoring treatment and control mesocosms for 4 days. Cyanobacteria dominated control mesocosms throughout the experiment while treatment mesocosms experienced a 99% reduction, as determined by bacterial amplicon sequencing, and a 92% reduction in bacterial cell density within 1 day post-treatment. Only the bacterial community exhibited signs of regrowth, with a fold change of 9.2 bacterial cell density from day 1 to day 2. Recovery consisted of succession by Planctomycetota (47%) and Gammaproteobacteria (17%), which were likely resilient due to passive cell component compartmentalization and rapid upregulation of dnaK and groEL oxidative stress genes, respectively. The altered microbiome retained beneficial functionality of microcystin degradation through a currently recognized but unidentified pathway in Gammaproteobacteria, resulting in a 70% reduction coinciding with bacterial regrowth. There was also an 81% reduction of both total nitrogen and phosphorus, as compared to 91 and 93% in the control, respectively, due to high expressions of genes related to nitrogen (argH, carB, glts, glnA) and phosphorus (pntAB, phoB, pstSCB) cycling. Overall, we found a portion of the bacterial community was resilient to the high-concentration hydrogen peroxide treatment, resulting in Planctomycetota and Gammaproteobacteria dominance. This high-concentration treatment may be suitable to rapidly end cHABs which have already negatively impacted the aquatic environment rather than allow them to persist.
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Affiliation(s)
- Taylor L Hancock
- School of Geosciences, University of South Florida, Tampa, FL 33620, United States; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Elizabeth K Dahedl
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Michael A Kratz
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Hidetoshi Urakawa
- School of Geosciences, University of South Florida, Tampa, FL 33620, United States; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States.
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23
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Unnikrishnan DK, Sreeharsha RV, Mudalkar S, Reddy AR. Flowering onset time is regulated by microRNA-mediated trehalose-6-phosphate signaling in Cajanus cajan L . under elevated CO 2. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:483-496. [PMID: 38633268 PMCID: PMC11018574 DOI: 10.1007/s12298-024-01434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
CO2 levels are known to have an impact on plant development and physiology. In the current study, we have investigated the effect of elevated CO2 on flowering and its regulation through miRNA mediated sugar signaling. We also unraveled small RNA transcriptome of pigeonpea under ambient and elevated CO2 conditions and predicted the targets for crucial miRNAs through computational methods. The results have shown that the delayed flowering in pigeonpea under elevated CO2 was due to an imbalance in C:N stoichiometry and differential expression pattern of aging pathway genes, including SQUAMOSA PROMOTER BINDING PROTEIN-LIKE. Furthermore, qRT PCR analysis has revealed the role of miR156 and miR172 in mediating trehalose-6-phosphate dependent flowering regulation. The current study is crucial in understanding the responses of flowering patterns in a legume crop to elevated CO2 which showed a significant impact on its final yields. Also, these findings are crucial in devising effective crop improvement strategies for developing climate resilient crops, including pigeonpea. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01434-9.
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Affiliation(s)
| | | | - Shalini Mudalkar
- Forest College and Research Institute, Hyderabad, Mulugu, Telangana 502279 India
| | - Attipalli R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500049 India
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24
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Baylous HR, Gladfelter MF, Gardner MI, Foley M, Wilson AE, Steffen MM. Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response. HARMFUL ALGAE 2024; 133:102575. [PMID: 38485434 DOI: 10.1016/j.hal.2024.102575] [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: 10/20/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/19/2024]
Abstract
Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.
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Affiliation(s)
- Hunter R Baylous
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Matthew F Gladfelter
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Malia I Gardner
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Madalynn Foley
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Morgan M Steffen
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA.
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25
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Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [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: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
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Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
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26
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Kumar B, Lorusso E, Fosso B, Pesole G. A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions. Front Microbiol 2024; 15:1343572. [PMID: 38419630 PMCID: PMC10900530 DOI: 10.3389/fmicb.2024.1343572] [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: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.
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Affiliation(s)
- Bablu Kumar
- Università degli Studi di Milano, Milan, Italy
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Erika Lorusso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
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27
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Real MVF, Colvin MS, Sheehan MJ, Moeller AH. Major urinary protein ( Mup) gene family deletion drives sex-specific alterations in the house-mouse gut microbiota. Microbiol Spectr 2024; 12:e0356623. [PMID: 38170981 PMCID: PMC10846032 DOI: 10.1128/spectrum.03566-23] [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: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiota is shaped by host metabolism. In house mice (Mus musculus), major urinary protein (MUP) pheromone production represents a considerable energy investment, particularly in sexually mature males. Deletion of the Mup gene family shifts mouse metabolism toward an anabolic state, marked by lipogenesis, lipid accumulation, and body mass increases. Given the metabolic implications of MUPs, they may also influence the gut microbiota. Here, we investigated the effect of a deletion of the Mup gene family on the gut microbiota of sexually mature mice. Shotgun metagenomics revealed distinct taxonomic and functional profiles between wild-type and knockout males but not females. Deletion of the Mup gene cluster significantly reduced diversity in microbial families and functions in male mice. Additionally, a species of Ruminococcaceae and several microbial functions, such as transporters involved in vitamin B5 acquisition, were significantly depleted in the microbiota of Mup knockout males. Altogether, these results show that MUPs significantly affect the gut microbiota of house mouse in a sex-specific manner.IMPORTANCEThe community of microorganisms that inhabits the gastrointestinal tract can have profound effects on host phenotypes. The gut microbiota is in turn shaped by host genes, including those involved with host metabolism. In adult male house mice, expression of the major urinary protein (Mup) gene cluster represents a substantial energy investment, and deletion of the Mup gene family leads to fat accumulation and weight gain in males. We show that deleting Mup genes also alters the gut microbiota of male, but not female, mice in terms of both taxonomic and functional compositions. Male mice without Mup genes harbored fewer gut bacterial families and reduced abundance of a species of Ruminococcaceae, a family that has been previously shown to reduce obesity risk. Studying the impact of the Mup gene family on the gut microbiota has the potential to reveal the ways in which these genes affect host phenotypes.
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Affiliation(s)
- Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Melanie S. Colvin
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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28
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Lahiani M, Gokulan K, Sutherland V, Cunny HC, Cerniglia CE, Khare S. Early Developmental Exposure to Triclosan Impacts Fecal Microbial Populations, IgA and Functional Activities of the Rat Microbiome. J Xenobiot 2024; 14:193-213. [PMID: 38390992 PMCID: PMC10885032 DOI: 10.3390/jox14010012] [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: 11/29/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 02/24/2024] Open
Abstract
Triclosan (TCS), a broad-spectrum antibacterial chemical, is detected in human urine, breast milk, amniotic fluid, and feces; however, little is known about its impact on the intestinal microbiome and host mucosal immunity during pregnancy and early development. Pregnant female rats were orally gavaged with TCS from gestation day (GD) 6 to postpartum (PP) day 28. Offspring were administered TCS from postnatal day (PND) 12 to 28. Studies were conducted to assess changes in the intestinal microbial population (16S-rRNA sequencing) and functional analysis of microbial genes in animals exposed to TCS during pregnancy (GD18), and at PP7, PP28 and PND28. Microbial abundance was compared with the amounts of TCS excreted in feces and IgA levels in feces. The results reveal that TCS decreases the abundance of Bacteroidetes and Firmicutes with a significant increase in Proteobacteria. At PND28, total Operational Taxonomic Units (OTUs) were higher in females and showed correlation with the levels of TCS and unbound IgA in feces. The significant increase in Proteobacteria in all TCS-treated rats along with the increased abundance in OTUs that belong to pathogenic bacterial communities could serve as a signature of TCS-induced dysbiosis. In conclusion, TCS can perturb the microbiome, the functional activities of the microbiome, and activate mucosal immunity during pregnancy and early development.
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Affiliation(s)
- Mohamed Lahiani
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Kuppan Gokulan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Vicki Sutherland
- National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC 27709, USA
| | - Helen C Cunny
- National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC 27709, USA
| | - Carl E Cerniglia
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sangeeta Khare
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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29
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Mashzhan A, Kistaubayeva A, Javier-López R, Bissenova U, Bissenbay A, Birkeland NK. Polycladomyces zharkentensis sp. nov., a novel thermophilic cellulose- and starch-degrading member of the Bacillota from a geothermal aquifer in Kazakhstan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38407242 DOI: 10.1099/ijsem.0.006269] [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] [Indexed: 02/27/2024] Open
Abstract
A thermophilic, aerobic and heterotrophic filamentous bacterium, designated strain ZKZ2T, was isolated from a pipeline producing hydrothermal water originating from a >2.3 km deep subsurface geothermal source in Zharkent, Almaty region, Kazakhstan. The isolate was Gram-stain-positive, non-motile, heat-resistant and capable of producing a variety of extracellular hydrolases. Growth occurred at temperatures between 55 and 75 °C, with an optimum around 70 °C, and at pH values between 5.5 and 9.0, with an optimum at pH 7.0-7.5 with the formation of aerial mycelia; endospores were produced along the aerial mycelium. The isolate was able to utilize the following substrates for growth: glycerol, l-arabinose, ribose, d-xylose, d-glucose, d-fructose, d-mannose, rhamnose, d-mannitol, methyl-d-glucopyranoside, aesculin, salicin, cellobiose, maltose, melibiose, sucrose, trehalose, melezitose, raffinose, starch, turanose and 5-keto-gluconate. Furthermore, it was able to hydrolyse carboxymethylcellulose, starch, skimmed milk, Tween 60 and Tween 80. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. Our 16S rRNA gene sequence analysis placed ZKZ2T within the genus Polycladomyces, family Thermoactinomycetaceae, with the highest similarity to the type species Polycladomyces abyssicola JIR-001T (99.18 % sequence identity). Our draft genome sequence analysis revealed a genome size of 3.3 Mbp with a G+C value of 52.5 mol%. The orthologous average nucleotide identity value as compared to that of its closest relative, P. abyssicola JIR-001T, was 90.23 %, with an in silico DNA-DNA hybridization value of 40.7 %, indicating that ZKZ2T represents a separate genome species. Based on the phenotypic and genome sequence differences from the other two Polycladomyces species, we propose that strain ZKZ2T represents a novel species, for which we propose the name Polycladomyces zharkentensis sp. nov. The type strain is ZKZ2T (=CECT 30708T=KCTC 43421T).
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Affiliation(s)
- Akzhigit Mashzhan
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
- Science Research Institute of Problem Biotechnology at the al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Zhahanger St. 14, 050054 Almaty, Kazakhstan
- Department of Botany, E.A. Buketov Karaganda State University, Universitet St. 28, 100028 Karaganda, Kazakhstan
| | - Aida Kistaubayeva
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
- Science Research Institute of Problem Biotechnology at the al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
| | - Rubén Javier-López
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Ulzhan Bissenova
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
| | - Akerke Bissenbay
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Zhahanger St. 14, 050054 Almaty, Kazakhstan
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
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30
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Aktar N, Mannan E, Kabir SMT, Hasan R, Hossain MS, Ahmed R, Ahmed B, Islam MS. Comparative metagenomics and microbial dynamics of jute retting environment. Int Microbiol 2024; 27:113-126. [PMID: 37204507 DOI: 10.1007/s10123-023-00377-7] [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: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.
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Affiliation(s)
- Nasima Aktar
- Basic and Applied Research on Jute, Dhaka, Bangladesh.
| | | | | | - Rajnee Hasan
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md Shahidul Islam
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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Babalola OO, Enagbonma BJ. Dataset of amplicon metagenomic assessment of barley rhizosphere bacteria under different fertilization regimes. Data Brief 2024; 52:109920. [PMID: 38186742 PMCID: PMC10770713 DOI: 10.1016/j.dib.2023.109920] [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: 04/12/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
The metagenomic dataset profiled in this research is built on bacterial 16S rRNA gene amplicon of DNA mined from barley rhizosphere under chemical (CB) and organic (OB) fertilization. Amplicon-based sequencing was prepared by the Illumina platform, and the raw sequence dataset was examined using Metagenomic Rast Server (MG-RAST). The metagenome comprised sixteen samples that include CB1 (494,583 bp), CB2 (586,532 bp), CB3 (706,685 bp), CB4 (574,606 bp), CB5 (395,460 bp), CB6 (520,822 bp), CB7 (511,729 bp), CB8 (548,074 bp), OB1 (642,794 bp), OB2 (513,767 bp), OB3 (461,293 bp), OB4 (498,241 bp), OB5 (689,497 bp), OB6 (423,436 bp), OB7 (478,657 bp) and OB8 (279,186 bp). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA827679 (CB1), PRJNA827686 (CB2), PRJNA827693 (CB3), PRJNA827699 (CB4), PRJNA827706 (CB5), PRJNA827761 (CB6), PRJNA827780 (CB7), PRJNA827786 (CB8), PRJNA826806 (OB1), PRJNA826824 (OB2), PRJNA826834 (OB3), PRJNA826841 (OB4), PRJNA826853 (OB5), PRJNA827254 (OB6), PRJNA827256 (OB7), and PRJNA827257 (OB8) at NCBI. Actinobacteria dominated the soil samples at the phylum level.
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Affiliation(s)
- Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Ben Jesuorsemwen Enagbonma
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
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Patel V, Patil K, Patel D, Kikani B, Madamwar D, Desai C. Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:208. [PMID: 38279971 DOI: 10.1007/s10661-024-12380-0] [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: 07/02/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.
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Affiliation(s)
- Vandan Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Kishor Patil
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Dishant Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Bhavtosh Kikani
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India.
| | - Chirayu Desai
- Department of Environmental Biotechnology, Gujarat Biotechnology University (GBU), Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India.
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Mefleh M, Omri G, Limongelli R, Minervini F, Santamaria M, Faccia M. Enhancing nutritional and sensory properties of plant-based beverages: a study on chickpea and Kamut® flours fermentation using Lactococcus lactis. Front Nutr 2024; 11:1269154. [PMID: 38328482 PMCID: PMC10847596 DOI: 10.3389/fnut.2024.1269154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
The study aimed to set up a protocol for the production of a clean-label plant-based beverage (PBB), obtained by mixing chickpeas and Kamut® flours and using a commercial Lactococcus lactis (LL) as fermentation starter, and to characterize it, from nutritional, microbiological, textural, shelf-life, and sensory points of view. The effect of using the starter was evaluated comparing the LL-PBB with a spontaneously fermented beverage (CTRL-PBB). Both PBBs were high in proteins (3.89/100 g) and could be considered as sources of fiber (2.06/100 g). Notably, L. lactis fermentation enhanced the phosphorus (478 vs. 331 mg/kg) and calcium (165 vs. 117 mg/kg) concentrations while lowering the raffinose content (5.51 vs. 5.08 g/100 g) compared to spontaneous fermentation. Cell density of lactic acid bacteria increased by ca. two log cycle during fermentation of LL-PBB, whereas undesirable microbial groups were not detected. Furthermore, L. lactis significantly improved the beverage's viscosity (0.473 vs. 0.231 Pa s), at least for 10 days, and lightness. To assess market potential, we conducted a consumer test, presenting the LL-PBB in "plain" and "sweet" (chocolate paste-added) variants. The "sweet" LL-PBB demonstrated a higher acceptability score than its "plain" counterpart, with 88 and 78% of participants expressing acceptability and a strong purchase intent, respectively. This positive consumer response positions the sweet LL-PBB as a valuable, appealing alternative to traditional flavored yogurts, highlighting its potential in the growing plant-based food market.
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Affiliation(s)
| | | | | | - Fabio Minervini
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
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Hartman WH, Bueno de Mesquita CP, Theroux SM, Morgan-Lang C, Baldocchi DD, Tringe SG. Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 2024; 9:e0093623. [PMID: 38170982 PMCID: PMC10804969 DOI: 10.1128/msystems.00936-23] [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: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.
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Affiliation(s)
| | | | | | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dennis D. Baldocchi
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Susannah G. Tringe
- DOE Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Zhou T, Xiao L, Zuo Z, Zhao F. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Res 2024; 52:D738-D746. [PMID: 37819042 PMCID: PMC10767955 DOI: 10.1093/nar/gkad813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Extensive evidence has demonstrated that the human microbiome and probiotics confer great impacts on human health, particularly during critical developmental stages such as pregnancy and infancy when microbial communities undergo remarkable changes and maturation. However, a major challenge in understanding the microbial community structure and interactions between mothers and infants lies in the current lack of comprehensive microbiome databases specifically focused on maternal and infant health. To address this gap, we have developed an extensive database called MAMI (Microbiome Atlas of Mothers and Infants) that archives data on the maternal and neonatal microbiome, as well as abundant resources on edible probiotic strains. By leveraging this resource, we can gain profound insights into the dynamics of microbial communities, contributing to lifelong wellness for both mothers and infants through precise modulation of the developing microbiota. The functionalities incorporated into MAMI provide a unique perspective on the study of the mother-infant microbiome, which not only advance microbiome-based scientific research but also enhance clinical practice. MAMI is publicly available at https://bioinfo.biols.ac.cn/mami/.
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Affiliation(s)
- Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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36
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Arora U, Khuntia HK, Chanakya HN, Kapley A. Luffa cylindrica (Sponge Gourd) Fibers in Treatment of Greywater: an Aerobic Fixed-Film Reactor Approach. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04804-3. [PMID: 38175410 DOI: 10.1007/s12010-023-04804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/05/2024]
Abstract
The need for potable water consumption in urban and suburban regions can be decreased by greywater treatment and its reuse. Utilizing natural fibers may provide sustainable solutions in addressing challenges related to water resource management. In this study, a fixed-film reactor was designed with Luffa cylindrica (an annually occurring fruit) as a bio-carrier. The lab-scale reactors were configured with and without Luffa cylindrica and were run for 90 days in fed-batch mode. Scanning electron microscopy (SEM) was performed to validate biofilm production over time. Monitoring COD, nitrogen, and total phosphate removal allowed for analysis of treatment effectiveness. Results demonstrated the treatment efficiency for the experimental reactor was 70.96%, 97.02%, 92.57%, and 81.20% for COD, nitrogen, phosphate, and anionic surfactant (AS), respectively. 16 s rRNA gene sequencing of bio-carrier and control greywater samples was carried out. Many bacteria known to break down anionic surfactants were observed, and microbial succession was witnessed in the control reactor vs. the experimental reactor samples. The three most prevalent genera in the experimental samples were Chlorobium, Chlorobaculum, and Terrimonas. However, it is crucial to underscore that additional research is essential to solidify our understanding in this domain, with this study laying the fundamental groundwork.
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Affiliation(s)
- Upasana Arora
- Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
| | - Himanshu Kumar Khuntia
- Centre for Sustainable Technologies, Indian Institute of Science, Bangalore, 560012, India
| | - H N Chanakya
- Centre for Sustainable Technologies, Indian Institute of Science, Bangalore, 560012, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India.
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37
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Dorlass EG, Amgarten DE. Bioinformatic Approaches for Comparative Analysis of Viruses. Methods Mol Biol 2024; 2802:395-425. [PMID: 38819566 DOI: 10.1007/978-1-0716-3838-5_13] [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] [Indexed: 06/01/2024]
Abstract
The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need adaptations. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. This chapter offers descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. The authors also provide comments and discussion on how viruses' unique features can affect standard analyses and how to overcome some of the major sources of problems. Protocols and topics emphasize online tools (which are more accessible to users) and give the real experience of what most bioinformaticians do in day-by-day work with command-line pipelines. The topics discussed include (1) clustering related genomes, (2) whole genome multiple sequence alignments for small RNA viruses, (3) protein alignment for marker genes and species affiliation, (4) variant calling and annotation, and (5) virome analyses and pathogen identification.
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Chai G, Li J, Li Z. The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics. Microbiol Res 2024; 278:127542. [PMID: 37979302 DOI: 10.1016/j.micres.2023.127542] [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: 08/03/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.
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Affiliation(s)
- Guangjun Chai
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Sánchez-Reyes A, Fernández-López MG. Sketched reference databases for genome-based taxonomy and comparative genomics. BRAZ J BIOL 2024; 84:e256673. [DOI: 10.1590/1519-6984.256673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 06/15/2022] [Indexed: 12/23/2022] Open
Abstract
Abstract The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor’s exploration and selection, among others.
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Brzeszcz J, Steliga T, Ryszka P, Kaszycki P, Kapusta P. Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5668-5683. [PMID: 38127231 PMCID: PMC10799122 DOI: 10.1007/s11356-023-31405-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Teresa Steliga
- Department of Production Technology of Reservoir Fluids, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
| | - Przemysław Ryszka
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Paweł Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, Al. Mickiewicza 21, 31-425, Kraków, Poland
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
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Johnson J, Jain KR, Patel A, Parmar N, Joshi C, Madamwar D. Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal. World J Microbiol Biotechnol 2023; 40:52. [PMID: 38146029 DOI: 10.1007/s11274-023-03848-1] [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: 03/04/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023]
Abstract
Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.
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Affiliation(s)
- Jenny Johnson
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Kunal R Jain
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Anand Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Nidhi Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, 6th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa (Anand), Gujarat, 388 421, India.
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42
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Wasti QZ, Sabar MF, Farooq A, Khan MU. Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00770-8. [PMID: 38147285 DOI: 10.1007/s12024-023-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.
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Affiliation(s)
- Qandeel Zaineb Wasti
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abeera Farooq
- Punjab University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
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Wei J, Lotfy P, Faizi K, Baungaard S, Gibson E, Wang E, Slabodkin H, Kinnaman E, Chandrasekaran S, Kitano H, Durrant MG, Duffy CV, Pawluk A, Hsu PD, Konermann S. Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting. Cell Syst 2023; 14:1087-1102.e13. [PMID: 38091991 DOI: 10.1016/j.cels.2023.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 05/03/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Effective and precise mammalian transcriptome engineering technologies are needed to accelerate biological discovery and RNA therapeutics. Despite the promise of programmable CRISPR-Cas13 ribonucleases, their utility has been hampered by an incomplete understanding of guide RNA design rules and cellular toxicity resulting from off-target or collateral RNA cleavage. Here, we quantified the performance of over 127,000 RfxCas13d (CasRx) guide RNAs and systematically evaluated seven machine learning models to build a guide efficiency prediction algorithm orthogonally validated across multiple human cell types. Deep learning model interpretation revealed preferred sequence motifs and secondary features for highly efficient guides. We next identified and screened 46 novel Cas13d orthologs, finding that DjCas13d achieves low cellular toxicity and high specificity-even when targeting abundant transcripts in sensitive cell types, including stem cells and neurons. Our Cas13d guide efficiency model was successfully generalized to DjCas13d, illustrating the power of combining machine learning with ortholog discovery to advance RNA targeting in human cells.
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Affiliation(s)
- Jingyi Wei
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kian Faizi
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Eleanor Wang
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Slabodkin
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Emily Kinnaman
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Sita Chandrasekaran
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Hugo Kitano
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Connor V Duffy
- Arc Institute, Palo Alto, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Silvana Konermann
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA.
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44
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community. Sci Rep 2023; 13:21741. [PMID: 38066117 PMCID: PMC10709317 DOI: 10.1038/s41598-023-49044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.
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Affiliation(s)
- Matevž Likar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Mateja Grašič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Blaž Stres
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Biocybernetics and Robotics, Department of Automation, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Regvar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Alenka Gaberščik
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
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45
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Li W, Wang L, Li X, Zheng X, Cohen MF, Liu YX. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1182-1194. [PMID: 36089219 PMCID: PMC11082258 DOI: 10.1016/j.gpb.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.
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Affiliation(s)
- Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Yong-Xin Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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46
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [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: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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47
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Akanmu AM, van Marle-Kӧster E, Hassen A, Adejoro FA. Datasets of shotgun metagenomics evaluation of rumen microbiota of South African mutton merino sheep. Data Brief 2023; 51:109629. [PMID: 37840986 PMCID: PMC10570938 DOI: 10.1016/j.dib.2023.109629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
The rumen microbial consortium plays a crucial role in the production performance and health of the ruminant animal. They are responsible for breaking down complex plant materials such as cellulose and hemicellulose to release usable energy by the host animal. Rumen microbial diversity manipulation through dietary strategies can be used to achieve several goals such as improved feed efficiency, reduced environmental impact or better utilization of low-quality forages. The dataset, deposited in the National Centre for Biotechnology Information SRA with project number PRJNA775821, comprises sequenced DNA extracted from the rumen content of 16 South African Merino sheep supplemented with different plant extracts. Illumina HiSeq™ 6000 technology was utilised to generate a total of approximately 46.7 Gb in raw nucleotide data. The data consists of 700,318,582 sequences, each with an average length of 184 base pairs. Taxonomic annotation conducted through the MG-RAST server showed the dominant phylum averages are Bacteroidetes (51 %) and Firmicutes (28 %), while Euryarchaeota, Actinobacteria, and Proteobacteria each account for approximately 3 % of the population. This dataset also enables us to identify and profile all expressed genes related to metabolic and chemical processes. The dataset is a valuable tool, offering insights that can lead to enhanced sustainability, profitability and reduced environmental impact within the context of ruminant production process.
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Affiliation(s)
| | | | - Abubeker Hassen
- Department of Animal Science, University of Pretoria, Pretoria 0028, South Africa
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48
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Zhao Y, Huang F, Wang W, Gao R, Fan L, Wang A, Gao SH. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165867. [PMID: 37516185 DOI: 10.1016/j.scitotenv.2023.165867] [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: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.
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Affiliation(s)
- Yanmei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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49
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Pioli S, Clagnan E, Chowdhury AA, Bani A, Borruso L, Ventura M, Tonon G, Brusetti L. Structural and functional microbial diversity in deadwood respond to decomposition dynamics. Environ Microbiol 2023; 25:2351-2367. [PMID: 37403552 DOI: 10.1111/1462-2920.16459] [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: 02/20/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.
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Affiliation(s)
- Silvia Pioli
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo (RM), Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Atif Aziz Chowdhury
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Alessia Bani
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Maurizio Ventura
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Giustino Tonon
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
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50
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Laux M, Piroupo CM, Setubal JC, Giani A. The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade. HARMFUL ALGAE 2023; 129:102518. [PMID: 37951618 DOI: 10.1016/j.hal.2023.102518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023]
Abstract
Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.
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Affiliation(s)
- Marcele Laux
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Carlos Morais Piroupo
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Alessandra Giani
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil.
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