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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Gonzalez-Pumariega M, Elez J, Duarte E, de la Rasilla M, Canaveras JC, Saiz-Jimenez C, Sanchez-Moral S. Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171137. [PMID: 38401719 DOI: 10.1016/j.scitotenv.2024.171137] [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: 09/30/2023] [Revised: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
A flood event affecting Pindal Cave, a UNESCO World Heritage site, introduced a substantial amount of external sediments and waste into the cave. This event led to the burial of preexisting sediments, altering the biogeochemical characteristics of the cave ecosystem by introducing heightened levels of organic matter, nitrogen compounds, phosphorus, and heavy metals. The sediments included particulate matter and waste from a cattle farm located within the water catchment area of the cavity, along with diverse microorganisms, reshaping the cave microbial community. This study addresses the ongoing influence of a cattle farm on the cave ecosystem and aims to understand the adaptive responses of the underground microbial community to the sudden influx of waste allochthonous material. Here, we show that the flood event had an immediate and profound effect on the cave microbial community, marked by a significant increase in methanogenic archaea, denitrifying bacteria, and other microorganisms commonly associated with mammalian intestinal tracts. Furthermore, our findings reveal that one year after the flood, microorganisms related to the flood decreased, while the increase in inorganic forms of ammonium and nitrate suggests potential nitrification, aligning with increased abundances of corresponding functional genes involved in nitrogen cycling. The results reveal that the impact of pollution was neither recent nor isolated, and it was decisive in stopping livestock activity near the cave. The influence of the cattle farm has persisted since its establishment over the impluvium area, and this influence endures even a year after the flood. Our study emphasizes the dynamic interplay between natural events, anthropogenic activities, and microbial communities, offering insights into the resilience of cave ecosystems. Understanding microbial adaptation in response to environmental disturbances, as demonstrated in this cave ecosystem, has implications for broader ecological studies and underscores the importance of considering temporal dynamics in conservation efforts.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Spanish Geological Survey (IGME-CSIC), 28003 Madrid, Spain.
| | | | | | - Javier Elez
- Department of Geology, University of Salamanca, 37008 Salamanca, Spain.
| | - Elsa Duarte
- Department of History, University of Oviedo, 33011 Oviedo, Spain
| | | | - Juan Carlos Canaveras
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet. Front Microbiol 2023; 14:1266025. [PMID: 38029196 PMCID: PMC10666647 DOI: 10.3389/fmicb.2023.1266025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | | | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
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Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples. Microorganisms 2023; 11:microorganisms11030660. [PMID: 36985233 PMCID: PMC10051802 DOI: 10.3390/microorganisms11030660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples—or in this case, chicken droppings.
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Singh T, Alhazmi A, Mohammad A, Srivastava N, Haque S, Sharma S, Singh R, Yoon T, Gupta VK. Integrated biohydrogen production via lignocellulosic waste: Opportunity, challenges & future prospects. BIORESOURCE TECHNOLOGY 2021; 338:125511. [PMID: 34274587 DOI: 10.1016/j.biortech.2021.125511] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen production through biological route is the cleanest, renewable and potential way to sustainable energy generation. Productions of hydrogen via dark and photo fermentations are considered to be more sustainable and economical approach over numerous existing biological modes. Nevertheless, both the biological modes suffer from certain limitations like low yield and production rate, and because of these practical implementations are still far away. Therefore, the present review provides an assessment and feasibility of integrated biohydrogen production strategy by combining dark and photo-fermentation as an advanced biochemical processing while using lignocellulosics biomass to improve and accelerate the biohydrogen production technology in a sustainable manner. This review also evaluates practical viability of the integrated approach for biohydrogen production along with the analysis of the key factors which significantly influence to elevate this technology on commercial ground with the implementation of various environment friendly and innovative approaches.
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Affiliation(s)
- Tripti Singh
- School of Biosciences IMS Ghaziabad UC Campus, Ghaziabad, Uttar Pradesh 201015, India
| | - Alaa Alhazmi
- Medical Laboratory Technology Department Jazan University, Jazan, Saudi Arabia; SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan, Saudi Arabia
| | - Akbar Mohammad
- School of Chemical Engineering, Yeungnam University, Gyeongsan-si, Gyeongbuk 38541, South Korea
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005 India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University Faculty of Medicine, Görükle Campus, 16059, Nilüfer, Bursa, Turkey
| | - Shalini Sharma
- School of Biosciences IMS Ghaziabad UC Campus, Ghaziabad, Uttar Pradesh 201015, India
| | - Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi 110052, India
| | - Taeho Yoon
- School of Chemical Engineering, Yeungnam University, Gyeongsan-si, Gyeongbuk 38541, South Korea
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
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Hu D, Yang J, Qi Y, Li B, Li K, Mok KM. Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment. Front Vet Sci 2021; 8:708512. [PMID: 34490397 PMCID: PMC8416479 DOI: 10.3389/fvets.2021.708512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jianming Yang
- Xinjiang Research Centre for Breeding Przewalski's Horse, Urumqi, China
| | - Yingjie Qi
- Xinjiang Kalamaili Ungulate Nature Reserve Management Center, Changji, China
| | - Boling Li
- China National Environment Monitoring Centre, Beijing, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Meng Mok
- Department of Civil and Environmental Engineering, University of Macau, Macao, China
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