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Chettri D, Verma AK. Statistical optimization of cellulase production from Bacillus sp. YE16 isolated from yak dung of the Sikkim Himalayas for its application in bioethanol production using pretreated sugarcane bagasse. Microbiol Res 2024; 281:127623. [PMID: 38301380 DOI: 10.1016/j.micres.2024.127623] [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: 07/06/2023] [Revised: 11/03/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024]
Abstract
Cellulolytic bacteria were isolated from yak dung samples collected from different habitats of Sikkim, India. Isolate YE16 from the Yumthang Valley sample showed highest enzyme activity of 7.68 U/mL and was identified as Bacillus sp., which has a sequence similarity of 96.15% with B. velezensis. One factor at a time (OFAT) analysis revealed that an acidic pH of 5 with 37 °C temperature was optimum for maximum enzyme production after 36 hrs of incubation (13.88 U/mL), which was further increased after statistical optimization (34.70 U/mL). Media optimization based on response surface methodology predicted that Carboxymethyl cellulose (CMC) and MgSO4 at concentrations of 30 g/L and 0.525 g/L, respectively, at pH 5.5 to show CMCase activity of 30.612 U/mL, which was consistent with the observed value of 30.25 U/mL and confirmed the model. The crude enzyme also efficiently hydrolyzed alkaline pretreated sugarcane bagasse, releasing 7.09 g/L of glucose equivalent with an ethanol production of 3.05 g.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India.
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Zhang J, Wei Y, Qiu H, Han J. TMT-based quantitative proteomics reveals the nutritional and stress resistance functions of anaerobic fungi in yak rumen during passage at different time intervals. Anaerobe 2024; 85:102805. [PMID: 38049048 DOI: 10.1016/j.anaerobe.2023.102805] [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: 05/09/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVES Anaerobic fungi are critical for nutrient digestion in the yak rumen. Although studies have reported the effects of passage at different time intervals on the community structure of yak rumen anaerobic fungi, it is unknown whether passage culture at different time intervals affects the microbial proteins of rumen anaerobic fungi and their functions. METHODS Mycelium was obtained using the anaerobic continuous batch culture (CBC) of yak rumen fluid at intervals of 3 d, 5 d and 7 d. Quantitative analysis of fungal proteins and functional analysis was performed using tandem mass tagging (TMT) and bioinformatics. RESULTS A total of 56 differential proteins (DPs) were found in 5 d vs. 3 d and 7 d vs. 3 d. Gene ontology (GO) enrichment indicated that the up-regulated proteins were mainly involved in biological regulation, cellular process, metabolic process, macromolecular complex, membrane, cell part, organelle, binding, catalytic activity and transporter activity. The downregulated proteins were mainly enriched in metabolic process, cell part, binding and catalytic activity. Furthermore, the downregulated proteins in 7 d vs. 3 d were related to membrane and organelle. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results indicated that DPs were enriched in 14 pathways in 5 d vs. 3 d and 7 d vs. 3 d, mainly including terpenoid backbone biosynthesis, alaine, aspartate and glutamate metabolism, arginine biosynthesis, hypotaurine, cyanoamino acid, glutathione, β-alanine, pyrimidine, purine, galactose and propanate metabolism, steroid biosynthesis, ribosome biogenesis in eukaryotes and aminoacyl tRNA biosynthesis. The DPs were enriched in only 2 pathways in 5 d vs 3 d, lysine biosynthesis and cysteine and methionine metabolism. N-glycan biosynthesis and retinol metabolism are only found in the metabolism of DPs in 7 d vs 3 d. CONCLUSIONS Yak rumen anaerobic fungal proteins are involved in nutrition and stress tolerance during passage at different time intervals.
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Affiliation(s)
- Jingrong Zhang
- College of Pratacultural, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yaqin Wei
- Institute of Biology, Gansu Academy of Science, Lanzhou, 730030, China
| | - Huizhen Qiu
- College of Pratacultural, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Jiayi Han
- Gansu Academy of Science, Lanzhou, 730030, China
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Wang S, Su M, Hu X, Wang X, Han Q, Yu Q, Heděnec P, Li H. Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny. FEMS Microbiol Lett 2024; 371:fnad135. [PMID: 38124623 DOI: 10.1093/femsle/fnad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.
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Affiliation(s)
- Sijie Wang
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Ming Su
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, 143 Xiangzhang East Road, Changsha, Hunan Province 410014, China
| | - Xueqian Hu
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, Gansu Province 730020, China
| | - Petr Heděnec
- Institute for Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Huan Li
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, Gansu Province 730020, China
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Liu X, Yang Z, Yang J, Wang D, Niu J, Bai B, Sun W, Ma S, Cheng Y, Hao L. A Comparative Study of Growth Performance, Blood Biochemistry, Rumen Fermentation, and Ruminal and Fecal Bacterial Structure between Yaks and Cattle Raised under High Concentrate Feeding Conditions. Microorganisms 2023; 11:2399. [PMID: 37894057 PMCID: PMC10609059 DOI: 10.3390/microorganisms11102399] [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: 09/08/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
This study compared the growth performance, serum biochemical indicators, rumen fermentation parameters, rumen bacterial structure, and fecal bacterial structure of cattle and yaks fed for two months and given a feed containing concentrate of a roughage ratio of 7:3 on a dry matter basis. Compared with cattle, yak showed better growth performance. The serum biochemical results showed that the albumin/globulin ratio in yak serum was significantly higher than that in cattle. Aspartate aminotransferase, indirect bilirubin, creatine kinase, lactate dehydrogenase, and total cholesterol were significantly lower in yaks than in cattle. The rumen pH, acetate to propionate ratio, and acetate were lower in yaks than in cattle, whereas the lactate in yaks was higher than in cattle. There were significant differences in the structure of ruminal as well as fecal bacteria between cattle and yaks. The prediction of rumen bacterial function showed that there was a metabolic difference between cattle and yaks. In general, the metabolic pathway of cattle was mainly riched in a de novo synthesis of nucleotides, whereas that of yaks was mainly riched in the metabolic utilization of nutrients. This study provides a basis for understanding a rumen ecology under the condition of a high concentrate diet.
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Affiliation(s)
- Xiaojing Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhanming Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Jinfen Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Dongyang Wang
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jianzhang Niu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Binqiang Bai
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Wu Sun
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Shike Ma
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
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Zhu Y, Sun G, Luosang-dunzhu, Li X, Luosang-zhaxi, Suolang-zhaxi, Suolang, Ciyang, Cidan-yangji, Basang-wangdui, Pan F, Peng Q. High energy level diet improves the growth performance and rumen fermentation of yaks in cold weather. Front Vet Sci 2023; 10:1212422. [PMID: 37546339 PMCID: PMC10402921 DOI: 10.3389/fvets.2023.1212422] [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: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023] Open
Abstract
To date, no research has been done on energy requirements for yaks in Tibetan cold weather. The findings of the current study provide proper energy requirements for yaks would facilitate scientific feeding of fattening yaks in cold weather. The metabolomics and 16s rRNA sequencing technologies were used to explore the underlying mechanism that affects the growth performance of yaks fed with different energy levels of diet in cold weather. Three groups of yaks (141.7 ± 3.34 kg) were fed with diets containing metabolizable energy 7.20, 7.89, and 8.58 MJ/kg DM (dry matter) and named the low-, medium-, and high-energy groups, respectively. The results showed that the average daily feed intake of the high-energy group was higher than that of the low-energy group (p = 0.006). Plasma aspartate aminotransferase (p = 0.004), alanine aminotransferase (p < 0.001), and interferon-γ (p < 0.001) in the high-energy group were lower than in the low-energy group. In contrast, superoxide dismutase (p < 0.001), immunoglobulin G (p < 0.001), and interleukin 2 (p = 0.002) were higher than the low-energy group. The rumen microbial protein (p = 0.025), total volatile fatty acids (p = 0.029), and neutral detergent fiber digestibility (p = 0.050) in the high-energy group were higher than in the low-energy group, whereas the acetate: propionate ratio (p = 0.001) and ammonium nitrogen (p = 0.001) were lower than in the low-energy group. The plasma metabolomics results displayed that yaks fed with a high-energy diet augmented the metabolism of arginine, proline, purine, taste transduction, pyrimidine, and glutathione pathways. The relative abundance of Methanobrevibacter in the high-energy group was lower (p < 0.001), whereas the relative abundance of Methanosphaera (p < 0.001) was higher than in the low-energy group. The results of the current study suggest that a high-energy diet in growing yaks during the cold season can improve growth performance, rumen microbial protein synthesis, antioxidants, and immunity.
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Affiliation(s)
- Yanbin Zhu
- Institute of Animal Science and Veterinary, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Guangming Sun
- Institute of Animal Science and Veterinary, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Luosang-dunzhu
- Institute of Animal Science and Veterinary, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Xin Li
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Luosang-zhaxi
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Suolang-zhaxi
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Suolang
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Ciyang
- Linzhou Animal Husbandry and Veterinary Station, Lhasa, China
| | - Cidan-yangji
- Institute of Animal Science and Veterinary, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Basang-wangdui
- Institute of Animal Science and Veterinary, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Feng Pan
- Institute of Animal Nutrition, Key Laboratory of Bovine Low-Carbon Farming and Safety Production, Sichuan Agricultural University, Chengdu, China
| | - Quanhui Peng
- Institute of Animal Nutrition, Key Laboratory of Bovine Low-Carbon Farming and Safety Production, Sichuan Agricultural University, Chengdu, China
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Thongbunrod N, Chaiprasert P. Anaerobic microbial cocktail of lignocellulolytic fungi and bacteria with methanogens for boosting methane production from unpretreated rice straw. Bioprocess Biosyst Eng 2023; 46:251-264. [PMID: 36495340 DOI: 10.1007/s00449-022-02829-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Rice straw (RS) has been recognized as a sustainable renewable energy resource for converting into sugars and volatile fatty acids (acetate, propionate, and butyrate) and subsequently to produce biogas. Enhanced production of these intermediates from RS by the different combinations of two consortia was investigated. Anaerobic microbial cocktails of fungi, bacteria, and methanogens were evaluated for performance and stability in the anaerobic digestion of untreated RS. The best-defined anaerobic microbial cocktail for high RS degradation and methane production, consisting of anaerobic bacteria (mainly Proteiniphilum acetatigenes, Pyramidobacter piscolens, and Mesotoga prima) and anaerobic lignocellulolytic/fermentative fungi (uncultured Neocallimastigales, Orpinomyces, Anaeromyces, and Feramyces sp.) at a copy number ratio of 103-105 copies/mL, including hydrogenotrophic and acetoclastic methanogens (Methanosarcina mazei, Methanoculleus marisnigri, Methanofollis liminatans, Methanoculleus bourgensis, and Methanosaeta harundinacea) concentration of 106 copies/mL, was successfully constructed. The system performance was 80% VS (volatile solids) RS degradation, 34 mL/day methane production rate, 318 mL/g VSadded methane yield, and a pH range of 6.90-7.70 within a short time of 14 days. A defined microbial cocktail has been proven as a potential alternative process for lignocellulose hydrolysis and methane production.
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Affiliation(s)
- Nitiya Thongbunrod
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Pawinee Chaiprasert
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Liu X, Gao J, Liu S, Cheng Y, Hao L, Liu S, Zhu W. The uniqueness and superiority of energy utilization in yaks compared with cattle in the highlands: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 12:138-144. [PMID: 36683881 PMCID: PMC9841238 DOI: 10.1016/j.aninu.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
Yaks living on the Qinghai-Tibetan Plateau for a long time have evolved a series of mechanisms to adapt to the unique geographical environment and climate characteristics of the plateau. Compared with other ruminants, yaks have higher energy utilization and metabolic efficiency. This paper presents possible mechanisms responsible for the efficient energy utilization, absorption and metabolism resulting from the unique evolutionary process of yaks. It is hoped that the information discussed in this review will give a better insight into the uniqueness and superiority of yaks in regards to energy metabolism and utilization compared with cattle and open new avenues for the targeted regulation of energy utilization pathways of other ruminants.
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Affiliation(s)
- Xiaojing Liu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Gao
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China,Corresponding authors.
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China,Corresponding authors.
| | - Shujie Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Li B, Jia G, Wen D, Zhao X, Zhang J, Xu Q, Zhao X, Jiang N, Liu Z, Wang Y. Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai–Tibetan plateau. Front Microbiol 2022; 13:1027138. [PMID: 36299720 PMCID: PMC9589358 DOI: 10.3389/fmicb.2022.1027138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
The grassland in the Qinghai–Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai–Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai–Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai–Tibetan plateau.
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Affiliation(s)
- Bin Li
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Agricultural College, Ningxia University, Yinchuan, China
| | - Gaobin Jia
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Dongxu Wen
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xiuxin Zhao
- Agricultural College, Ningxia University, Yinchuan, China
| | - Junxing Zhang
- Agricultural College, Ningxia University, Yinchuan, China
| | - Qing Xu
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Xialing Zhao
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Nan Jiang
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Zhenjiang Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Yachun Wang
- Agricultural College, Ningxia University, Yinchuan, China
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Wei Y, Yang H, Wang Z, Zhao J, Qi H, Wang C, Zhang J, Yang T. Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks. AMB Express 2022; 12:123. [PMID: 36121525 PMCID: PMC9485394 DOI: 10.1186/s13568-022-01462-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Anaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.
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Affiliation(s)
- Yaqin Wei
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jiang Zhao
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Hongshan Qi
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chuan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730000, People's Republic of China
| | - Jingrong Zhang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
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10
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Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment. Microorganisms 2022; 10:microorganisms10081550. [PMID: 36013968 PMCID: PMC9413874 DOI: 10.3390/microorganisms10081550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022] Open
Abstract
Diet has been suggested to be an important driver of variation in microbiota composition in mammals. However, whether this is a more general phenomenon and how fast changes in gut microbiota occur with changes in diet remains poorly understood. Forty-nine years ago, ten lizards of the species Podarcis siculus were taken from the island of Pod Kopište and introduced onto the island of Pod Mrčaru (Croatia). The introduced population underwent a significant dietary shift, and their descendants became omnivorous (consuming up to 80% plant material during summer). Variation in their gut microbiota has never been investigated. To elucidate the possible impact on the gut microbiota of this rapid change in diet, we compared the microbiota (V4 region of the 16S rRNA gene) of P. siculus from Pod Mrčaru, Pod Kopište, and the mainland. In addition, we explored other drivers of variation in gut microbiota including insularity, the population of origin, and the year of sampling. Alpha-diversity analyses showed that the microbial diversity of omnivorous lizards was higher than the microbial diversity of insectivorous lizards. Moreover, omnivorous individuals harbored significantly more Methanobrevibacter. The gut microbial diversity of insectivorous lizards was nonetheless more heterogeneous. Insectivorous lizards on the mainland had different gut microbial communities than their counterparts on the island of Pod Kopište. Bacillus and Desulfovibrio were more abundant in the gut microbiota from insular lizards compared to mainland lizards. Finally, we showed that the population of origin was also an important driver of the composition of the gut microbiota. The dietary shift that occurred in the introduced population of P. siculus has had a detectable impact on the gut microbiota, but other factors such as insularity and the population of origin also contributed to differences in the gut microbial composition of these lizards, illustrating the multifactorial nature of the drivers of variation in gut microbiota. Overall, our data show that changes in gut microbiota may take place on ecological timescales. Yet, diet is only one of many factors driving variation in gut microbiota across populations.
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Kazemi Shariat Panahi H, Dehhaghi M, Guillemin GJ, Gupta VK, Lam SS, Aghbashlo M, Tabatabaei M. A comprehensive review on anaerobic fungi applications in biofuels production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154521. [PMID: 35292323 DOI: 10.1016/j.scitotenv.2022.154521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic fungi (Neocallimastigomycota) are promising lignocellulose-degrading microorganisms that can be exploited by the biofuel industry. While natural production of ethanol by these microorganisms is very low, there is a greater potential for their use in the biogas industry. More specifically, anaerobic fungi can contribute to biogas production by either releasing holocellulose or reducing sugars from lignocelluloses that can be used as a substrate by bacteria and methanogens involved in the anaerobic digestion (AD) process or by metabolizing acetate and formate that can be directly consumed by methanogens. Despite their great potential, the appropriate tools for engineering anaerobic fungi have not been established yet. The first section of this review justifies how the biofuel industry can benefit from using anaerobic fungi and is followed by their taxonomy. In the third section, the possibility of using anaerobic fungi for the consolidated production of bioethanol is briefly discussed. Nevertheless, the main focus of this review is on the upstream and mainstream effects of bioaugmentation with anaerobic fungi on the AD process. The present review also scrutinizes the constraints on the way of efficient engineering of anaerobic rumen fungi. By providing this knowledge, this review aims to help research in this field with identifying the challenges that must be addressed by future experiments to achieve the full potentials of these promising microorganisms. To sum up, the pretreatment of lignocelluloses by anaerobic fungi can prevent carbohydrate loss due to respiration (compared to white-rot fungi). Following fungal mixed acid fermentation, the obtained slurry containing sugars and more susceptible holocellulose can be directly consumed by AD microorganisms (bacteria, methanogens). The bioaugmentation of anaerobic fungi into the AD process can increase methane biosynthesis by >3.3 times. Despite this, for the commercial AD process, novel genetic engineering techniques and kits must be developed to efficiently improve anaerobic fungi viability throughout the AD process.
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Affiliation(s)
- Hamed Kazemi Shariat Panahi
- Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China; Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia
| | - Mona Dehhaghi
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia; PANDIS.org, Australia
| | - Gilles J Guillemin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; PANDIS.org, Australia
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Centre for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mortaza Aghbashlo
- Department of Mechanical Engineering of Agricultural Machinery, Faculty of Agricultural Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China; Biofuel Research Team (BRTeam), Terengganu, Malaysia.
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12
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The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem. Animals (Basel) 2022; 12:ani12040412. [PMID: 35203120 PMCID: PMC8868365 DOI: 10.3390/ani12040412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/08/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary The donkey hindgut is a microbial-rich ecosystem in which caecum and colon fungi play an important role in dietary fiber degradation. In addition, the fibrolytic enzymes produced by hindgut microorganisms are key to the ability of equines to hydrolysis plant fiber. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. The dorsal colon presented a higher fibrolytic enzyme activity in comparison with caecum. The fungal community composition along donkey caecum and colon was determined by sequencing an internal transcribed spacer region (ITS) using Illumina MiSeq. The predominant fungi at phylum level were Ascomycota, Basidiomycota, and Neocallimastigomycota. The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum. The relative abundance of enzymes related to plant cell wall breakdown were also predicted by PICRUSt, and they were also greater in donkey colon than in caecum. The present study provided new information about fibrolytic enzyme profiles and fungal communities in donkey hindgut. The findings could therefore contribute to the further understanding of the fungal taxa and their dietary fiber degradation mechanisms in donkey hindgut ecosystem. Abstract The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.
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Li Y, Meng Z, Xu Y, Shi Q, Ma Y, Aung M, Cheng Y, Zhu W. Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials. Microorganisms 2021; 9:190. [PMID: 33477342 PMCID: PMC7830786 DOI: 10.3390/microorganisms9010190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
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Ferraro A, Massini G, Mazzurco Miritana V, Rosa S, Signorini A, Fabbricino M. A novel enrichment approach for anaerobic digestion of lignocellulosic biomass: Process performance enhancement through an inoculum habitat selection. BIORESOURCE TECHNOLOGY 2020; 313:123703. [PMID: 32580121 DOI: 10.1016/j.biortech.2020.123703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Inocula enrichment was performed using an innovative habitat-based selection approach to improve wheat straw (WS) anaerobic digestion (AD) efficiency. The procedure was carried out by sequentially re-inoculating the primary microbial community seven times in subsequent anaerobic reactors containing untreated WS. Re-inocula were performed at different re-inoculum times (24, 48, and 96 h) by moving a porous support mimicking a rumen structure from one batch to the next (S-tests) or re-inoculating only the culture medium (C-tests). Highest H2 production yields were observed after four and five re-inocula (0.08 ± 0.02 NmL h-1 gVS-1 and 0.09 ± 0.02 NmL h-1 gVS-1) for S-24 and S-48, respectively. For S-96, higher CH4 yields were observed after the start-up test and sixth re-inoculum (0.05 ± 0.003 NmL h-1 gVS-1 and 0.04 ± 0.005 NmL h-1 gVS-1, respectively). Accordingly, S-96 showed the highest active Archaea component (7%). C-test microbial communities were dominated by fermenting, hydrogen-producing bacteria and showed lower microbial community diversity than S-tests.
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Affiliation(s)
- Alberto Ferraro
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy.
| | - Giulia Massini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Valentina Mazzurco Miritana
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Silvia Rosa
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Antonella Signorini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy
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Li Y, Hou Z, Shi Q, Cheng Y, Zhu W. Methane Production From Different Parts of Corn Stover via a Simple Co-culture of an Anaerobic Fungus and Methanogen. Front Bioeng Biotechnol 2020; 8:314. [PMID: 32426337 PMCID: PMC7204275 DOI: 10.3389/fbioe.2020.00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
To determine ways to improve the utilization of corn stover, this study investigated methane production from different parts of corn stover using a simple co-culture of an anaerobic fungus (Pecoramyces species) and methanogen (Methanobrevibacter species). The simple co-culture was incubated with the stem pith, leaf blade, or stem bark of corn stover (as substrates) at 39°C for 72 h. The results showed that the stem bark had the lowest (P < 0.05) digestibility (38.0 ± 1.36%) and neutral detergent solubles, that is, cell solubles (31.6 ± 0.45%), and the highest (P < 0.05) lignin content (4.8 ± 0.56%). The leaf blade had a significantly higher methane conversion rate (56.6 ± 0.76 mL/g digested substrate) than the stem pith (49.2 ± 1.60 mL/g digested substrate), even though they showed similar levels of methane production (42.4 ± 1.0 mL and 40.9 ± 1.35 mL, respectively). Both the leaf blade and stem pith of corn stover have the potential to produce methane in a simple co-culture of an anaerobic fungus and methanogen.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Zhesheng Hou
- College of Mechanical and Electrical Engineering, Jilin Institute of Chemical Technology, Jilin, China
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
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Vinzelj J, Joshi A, Insam H, Podmirseg SM. Employing anaerobic fungi in biogas production: challenges & opportunities. BIORESOURCE TECHNOLOGY 2020; 300:122687. [PMID: 31926794 DOI: 10.1016/j.biortech.2019.122687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 05/24/2023]
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to efficiently break down lignocellulosic biomass. Their unique combination of mechanical and enzymatic attacks on recalcitrant plant structures bears great potential for enhancement of the anaerobic digestion (AD) process. Although scientists in this field have long agreed upon the potential of AF for biotechnology, research is only recently gaining traction. This delay was largely due to difficulties in culture-dependent and culture-independent analysis of those high-maintenance organisms with their still unknown complex growth requirements. In this review, we will summarize current research efforts on bioaugmentation with AF and further point out, how the lack of basic knowledge on AF nutritional needs hampers their implementation on an industrial scale. Through this, we hope to further kindle interest into basic research on AF in order to advance their stable integration into biotechnological processes.
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Affiliation(s)
- Julia Vinzelj
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Akshay Joshi
- ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
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17
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Langda S, Zhang C, Zhang K, Gui B, Ji D, Deji C, Cuoji A, Wang X, Wu Y. Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture. Animals (Basel) 2020; 10:ani10020186. [PMID: 31978949 PMCID: PMC7070549 DOI: 10.3390/ani10020186] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tibetan goats and sheep graze together but have different growth performances, immune responses, and feeding preferences in the Tibetan pasture. Rumen microbiota composed of bacteria, fungi, and protozoa are necessary for a healthy ruminant. Therefore, in this study, we comprehensively describe composition and diversity of bacteria, fungi, and protozoa in the high- altitude rumen. Compared with sheep, the bacteria that degrade crude protein and produce volatile fatty acids (VFA) were increased in the rumen of goats (Saccharofermentans and Lachnospiraceae_XPB1014) (p < 0.05). In addition, when compared with goats, the fungi and protozoa that degrade fiber were increased in rumen of sheep (Neocallimastigaceae and Metadinium) (p < 0.05). Furthermore, VFA were significantly increased in the rumen of goats compared with sheep (p < 0.05). The VFA level was consistent with differences in the microbiota composition in the rumen between goats and sheep. Under mixed grazing conditions, goats tend to select a high-crude protein diet that is good for growth, whereas sheep tend to select a high-lignin diet that is difficult to digest. Therefore, the different microbiota in the rumen of goats and sheep may be explained by dietary preference. Abstract Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.
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Affiliation(s)
- Suo Langda
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
| | - Ba Gui
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - De Ji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Ciren Deji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Awang Cuoji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
- Correspondence: (X.W.); (Y.W.)
| | - Yujiang Wu
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
- Correspondence: (X.W.); (Y.W.)
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Li Y, Sun M, Li Y, Cheng Y, Zhu W. Co-cultured methanogen improved the metabolism in the hydrogenosome of anaerobic fungus as revealed by gas chromatography-mass spectrometry analysis. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1948-1956. [PMID: 32054157 PMCID: PMC7649409 DOI: 10.5713/ajas.19.0649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/06/2020] [Indexed: 11/27/2022]
Abstract
Objective The purpose of this study was to reveal the metabolic shift in the fungus co-cultured with the methanogen (Methanobrevibacter thaueri). Methods Gas chromatography-mass spectrometry was used to investigate the metabolites in anaerobic fungal (Pecoramyces sp. F1) cells and the supernatant. Results A total of 104 and 102 metabolites were detected in the fungal cells and the supernatant, respectively. The partial least squares-discriminant analysis showed that the metabolite profiles in both the fungal cell and the supernatant were distinctly shifted when co-cultured with methanogen. Statistically, 16 and 30 metabolites were significantly (p<0.05) affected in the fungal cell and the supernatant, respectively by the co-cultured methanogen. Metabolic pathway analysis showed that co-culturing with methanogen reduced the production of lactate from pyruvate in the cytosol and increased metabolism in the hydrogenosomes of the anaerobic fungus. Citrate was accumulated in the cytosol of the fungus co-cultured with the methanogen. Conclusion The co-culture of the anaerobic fungus and the methanogen is a good model for studying the microbial interaction between H2-producing and H2-utilizing microorganisms. However, metabolism in hydrogenosome needs to be further studied to gain better insight in the hydrogen transfer among microorganisms.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Meizhou Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Wang H, Li P, Liu X, Zhang C, Lu Q, Xi D, Yang R, Wang S, Bai W, Yang Z, Zhou R, Cheng X, Leng J. The Composition of Fungal Communities in the Rumen of Gayals ( Bos frontalis), Yaks ( Bos grunniens), and Yunnan and Tibetan Yellow Cattle ( Bos taurs). Pol J Microbiol 2019; 68:505-514. [PMID: 31880894 PMCID: PMC7260705 DOI: 10.33073/pjm-2019-050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Affiliation(s)
- Houfu Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Pengfei Li
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Xuchuan Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Chunyong Zhang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Qiongfen Lu
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Renhui Yang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Shuling Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Wenshun Bai
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Zhen Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Rongkang Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Xiao Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Jing Leng
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
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Ferraro A, Massini G, Mazzurco Miritana V, Signorini A, Race M, Fabbricino M. A simplified model to simulate bioaugmented anaerobic digestion of lignocellulosic biomass: Biogas production efficiency related to microbiological data. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:885-895. [PMID: 31326812 DOI: 10.1016/j.scitotenv.2019.07.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Mathematical model applications for the bioaugmented anaerobic digestion (BAD) process seem to be lacking in the scientific literature, even more so when related to microbiological data. The present study suggests a simplified mathematical model to investigate and simulate the process kinetics of bioaugmented anaerobic digestion (BAD) aimed at improving biogas production from wheat straw (WS). Bioaugmented conditions were obtained through a mixed inoculum of anaerobic ruminal fungi (ARF) and hydrogen-producing fermenting bacteria (F210) added to a methanogenic inoculum. The investigation focused on two process configurations characterized by a mono (I-BAD) and two-stage (II-BAD) process and a conventional anaerobic digestion (AD) control test. Each configuration was used on two operating scales (i.e., 120 ml and 12,000 ml reactor volume) to provide different data sets for the calibration and validation of the mathematical model proposed. The model calibration step was used to determine the optimal values of selected parameters displaying higher significance for experimental result predictability. The model calibration results highlighted a similar behavior for both BAD tests, which was further strengthened by a statistical analysis supporting the observed correlation regardless of the BAD configuration involved. The BAD configuration always enhanced the CH4 production (>70%) with a faster kinetic in the II-BAD test. The microbiological results support the superior performance of the II-BAD test, displaying higher Archaea fractions (up to 14.5% on day 23) with values more than double compared to I-BAD and triple compared to the AD test. Furthermore, the presence of Methanosarcina inside the Archaea guild (6.4% and 4.5% at days 11 and 61, respectively) ensures a greater diversification of the metabolic pathways and supports the strength of the process performance. Cell density values are strongly in line with these results.
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Affiliation(s)
- Alberto Ferraro
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy.
| | - Giulia Massini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Valentina Mazzurco Miritana
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Antonella Signorini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123 Rome, Italy
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via di Biasio 43, 03043 Cassino, Italy
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125 Naples, Italy
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21
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Shi Q, Li Y, Li Y, Cheng Y, Zhu W. Effects of steam explosion on lignocellulosic degradation of, and methane production from, corn stover by a co-cultured anaerobic fungus and methanogen. BIORESOURCE TECHNOLOGY 2019; 290:121796. [PMID: 31319215 DOI: 10.1016/j.biortech.2019.121796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 05/23/2023]
Abstract
The aim of this study was to investigate the effects of steam explosion on lignocellulose digestibility of, and methane production from corn stover by a co-culture of anaerobic fungus and methanogen. The cumulative methane production at 72 h of incubation from the steam-exploded corn stover was 32.2 ± 1.74 mL, which not significantly different (P > 0.05) from that of the untreated corn stover (37.1 ± 1.09 mL). However, steam explosion decreased the hemicellulose contents of corn stover by 28.0 ± 0.39% and increased the neutral detergent solute by 23.5 ± 0.25%. While this treatment did not affect the dry matter digestibility (64.1 ± 0.26%, and 64.1 ± 0.28%, respectively). In conclusion, the co-culture of anaerobic fungus and methanogen can degrade the crude fibrous portion of corn stover without any pretreatments. It possesses promising biotechnological prospects for conversion of crop residue based straw resources to obtain biofuel in the form of methane.
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Affiliation(s)
- Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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22
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Botto E, Gioia L, Menéndez MDP, Rodríguez P. Pseudozyma sp. isolation from Eucalyptus leaves and its hydrolytic activity over xylan. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes. J Ind Microbiol Biotechnol 2019; 46:1427-1433. [PMID: 31089985 DOI: 10.1007/s10295-019-02188-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
Anaerobic gut fungi are biomass degraders that form syntrophic associations with other microbes in their native rumen environment. Here, RNA-Seq was used to track and quantify carbohydrate active enzyme (CAZyme) transcription in a synthetic consortium composed of the anaerobic fungus Anaeromyces robustus with methanogen Methanobacterium bryantii. Approximately 5% of total A. robustus genes were differentially regulated in co-culture with M. bryantii relative to cultivation of A. robustus alone. We found that 105 CAZymes (12% of the total predicted CAZymes of A. robustus) were upregulated while 29 were downregulated. Upregulated genes encode putative proteins with a wide array of cellulolytic, xylanolytic, and carbohydrate transport activities; 75% were fused to fungal dockerin domains, associated with a carbohydrate binding module, or both. Collectively, this analysis suggests that co-culture of A. robustus with M. bryantii remodels the transcriptional landscape of CAZymes and associated metabolic pathways in the fungus to aid in lignocellulose breakdown.
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24
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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25
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Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:9319345. [PMID: 30410420 PMCID: PMC6206559 DOI: 10.1155/2018/9319345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/22/2018] [Indexed: 11/18/2022]
Abstract
Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.
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26
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The biotechnological potential of anaerobic fungi on fiber degradation and methane production. World J Microbiol Biotechnol 2018; 34:155. [PMID: 30276481 DOI: 10.1007/s11274-018-2539-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 01/16/2023]
Abstract
Anaerobic fungi (phylum Neocallimastigomycota), an early branching family of fungi, are commonly encountered in the digestive tract of mammalian herbivores. To date, isolates from ten described genera have been reported, and several novel taxonomic groupings are detected using culture-independent molecular methods. Anaerobic fungi are recognized as playing key roles in the decomposition of lignocellulose (up to 50% of the ingested and untreated lignocellulose), with their physical penetration and extracellular enzymatical secretion of an unbiased diverse repertoire of cell-wall-degrading enzymes. The secreted cell-wall-degrading enzymes of anaerobic fungi include both free enzymes and extracellular multi-enzyme complexes called cellulosomes, both of which have potential as fiber degraders in industries. In addition, anaerobic fungi can provide large amounts of substrates such as hydrogen, formate, and acetate for their co-cultured methanogens. Consequently, large amounts of methane can be produced. And thus, it is promising to use the co-culture of anaerobic fungi and methanogens in the biogas process to intensify the biogas yield owing to the efficient and robust degradation of recalcitrant biomass by anaerobic fungi and improved methane production from co-cultures of anaerobic fungi and methanogens.
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27
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Xue D, Chen H, Luo X, Guan J, He Y, Zhao X. Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone. J Microbiol 2018; 56:734-743. [PMID: 30136259 DOI: 10.1007/s12275-018-8133-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 11/26/2022]
Abstract
The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.
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Affiliation(s)
- Dan Xue
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China.
| | - Xiaolin Luo
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, P. R. China.
| | - Jiuqiang Guan
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, P. R. China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China
| | - Xinquan Zhao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810008, P. R. China
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28
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Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ 2018; 6:e4276. [PMID: 29404209 PMCID: PMC5796279 DOI: 10.7717/peerj.4276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 12/25/2022] Open
Abstract
Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
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Affiliation(s)
- Shelby S Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Nicole C Elledge
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Current affiliation: University of Texas A&M Corpus Christi, Department of Life Sciences, Marine Biology Program, USA
| | - Katherine E Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Wei YQ, Yang HJ, Long RJ, Wang ZY, Cao BB, Ren QC, Wu TT. Characterization of natural co-cultures of Piromyces with Methanobrevibacter ruminantium from yaks grazing on the Qinghai-Tibetan Plateau: a microbial consortium with high potential in plant biomass degradation. AMB Express 2017; 7:160. [PMID: 28789484 PMCID: PMC5545993 DOI: 10.1186/s13568-017-0459-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 11/10/2022] Open
Abstract
Anaerobic fungi reside in the gut of herbivore and synergize with associated methanogenic archaea to decompose ingested plant biomass. Despite their potential for use in bioconversion industry, only a few natural fungus–methanogen co-cultures have been isolated and characterized. In this study we identified three co-cultures of Piromyces with Methanobrevibacter ruminantium from the rumen of yaks grazing on the Qinghai Tibetan Plateau. The representative co-culture, namely (Piromyces + M. ruminantium) Yak-G18, showed remarkable polysaccharide hydrolase production, especially xylanase. Consequently, it was able to degrade various lignocellulose substrates with a biodegrading capability superior to most previously identified fungus or fungus–methanogen co-culture isolates. End-product profiling analysis validated the beneficial metabolic impact of associated methanogen on fungus as revealed by high-yield production of methane and acetate and sustained growth on lignocellulose. Together, our data demonstrated a great potential of (Piromyces + M. ruminantium) Yak-G18 co-culture for use in industrial bioconversion of lignocellulosic biomass.
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30
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Ishaq SL, AlZahal O, Walker N, McBride B. An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation. Front Microbiol 2017; 8:1943. [PMID: 29067009 PMCID: PMC5641310 DOI: 10.3389/fmicb.2017.01943] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/21/2017] [Indexed: 01/08/2023] Open
Abstract
Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.
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Affiliation(s)
| | | | | | - Brian McBride
- Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Edwards JE, Forster RJ, Callaghan TM, Dollhofer V, Dagar SS, Cheng Y, Chang J, Kittelmann S, Fliegerova K, Puniya AK, Henske JK, Gilmore SP, O'Malley MA, Griffith GW, Smidt H. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. Front Microbiol 2017; 8:1657. [PMID: 28993761 PMCID: PMC5622200 DOI: 10.3389/fmicb.2017.01657] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022] Open
Abstract
Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.
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Affiliation(s)
- Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Robert J. Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Tony M. Callaghan
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | - Veronika Dollhofer
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | | | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural UniversityNanjing, China
| | - Jongsoo Chang
- Department of Agricultural Science, Korea National Open UniversitySeoul, South Korea
| | - Sandra Kittelmann
- Grasslands Research Centre, AgResearch Ltd.Palmerston North, New Zealand
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics, Czech Academy of SciencesPrague, Czechia
| | - Anil K. Puniya
- College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences UniversityLudhiana, India
- Dairy Microbiology Division, ICAR-National Dairy Research InstituteKarnal, India
| | - John K. Henske
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Sean P. Gilmore
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Gareth W. Griffith
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
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Li Y, Jin W, Mu C, Cheng Y, Zhu W. Indigenously associated methanogens intensified the metabolism in hydrogenosomes of anaerobic fungi with xylose as substrate. J Basic Microbiol 2017; 57:933-940. [PMID: 28791723 DOI: 10.1002/jobm.201700132] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/22/2017] [Accepted: 06/25/2017] [Indexed: 01/14/2023]
Abstract
Anaerobic fungi are potent lignocellulose degraders, but have not yet been exploited in this capacity, largely owing to their poor metabolic characterization. In the current study, a time course of fermentation was conducted to study the effect of the co-cultured methanogens on xylose metabolism by anaerobic fungi. The fermentation end-products from anaerobic fungal monoculture were H2 (6.7 ml), CO2 (65.7 ml), formate (17.90 mM), acetate (9.00 mM), lactate (11.89 mM), ethanol, and malate after 96 h fermentation. Compared to the monoculture, the end-products of co-culture shifted to more CO2 (71.8 ml) and acetate (15.20 mM), methane (14.9 ml), less lactate (5.28 mM), and hardly detectable formate and H2 at the end of fermentation. After 48 h, accumulated formate was remarkably consumed by co-cultured methanogens, accompanied by significantly increased acetate, CO2 and pH, and decreased lactate and malate. Xylose utilization, in both cultures, was similar during fermentation. However, the relative flux of carbon in hydrogenosomes in the co-culture was higher than that in the monoculture. In conclusion, the co-culture with methanogens enhanced "energy yields" of anaerobic fungi by removing the accumulated formate, decreased the metabolism in cytosol, for example, the lactate pathway, and increased the metabolism in hydrogenosomes, for example, the acetate pathway.
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Affiliation(s)
- Yuanfei Li
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Jin
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chunlong Mu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yanfen Cheng
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Weiyun Zhu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Mach N, Foury A, Kittelmann S, Reigner F, Moroldo M, Ballester M, Esquerré D, Rivière J, Sallé G, Gérard P, Moisan MP, Lansade L. The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology. Front Physiol 2017; 8:535. [PMID: 28790932 PMCID: PMC5524898 DOI: 10.3389/fphys.2017.00535] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method. In the P method, mares were separated from foals at progressively increasing intervals every day, starting from five min during the fourth week prior to weaning and ending with 6 h during the last week before weaning. In the A method, mares and foals were never separated prior to weaning (0 d). Different host phenotypes and gut microbiota composition were studied across 6 age strata (days -30, 0, 3, 5, 7, and 30 after weaning) by 16S rRNA gene sequencing. Results revealed that the beneficial species belonging to Prevotella, Paraprevotella, and Ruminococcus were more abundant in the A group prior to weaning compared to the P group, suggesting that the gut microbiota in the A cohort was better adapted to weaning. Streptococcus, on the other hand, showed the opposite pattern after weaning. Fungal loads, which are thought to increase the capacity for fermenting the complex polysaccharides from diet, were higher in P relative to A. Beyond the effects of weaning methods, maternal separation at weaning markedly shifted the composition of the gut microbiota in all foals, which fell into three distinct community types at 3 days post-weaning. Most genera in community type 2 (i.e., Eubacterium, Coprococcus, Clostridium XI, and Blautia spp.) were negatively correlated with salivary cortisol levels, but positively correlated with telomere length and N-butyrate production. Average daily gain was also greater in the foals harboring a community type 2 microbiota. Therefore, community type 2 is likely to confer better stress response adaptation following weaning. This study identified potential microbial biomarkers that could predict the likelihood for physiological adaptations to weaning in horses, although causality remains to be addressed.
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Affiliation(s)
- Núria Mach
- UMR 1313, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Aline Foury
- UMR 1286, Institut National de la Recherche Agronomique, Université Bordeaux, Nutrition et Neurobiologie IntégréeBordeaux, France
| | - Sandra Kittelmann
- AgResearch Ltd, Grasslands Research CentrePalmerston North, New Zealand
| | - Fabrice Reigner
- UMR 1282, Institut National de la Recherche Agronomique, Infectiologie et Santé PubliqueNouzilly, France
| | - Marco Moroldo
- UMR 1313, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries, Torre MarimonCaldes de Montbui, Spain
| | - Diane Esquerré
- UMR 444, Institut National de la Recherche Agronomique, Plateforme GETCastanet-Tolosan, France
| | - Julie Rivière
- UMR 1313, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Guillaume Sallé
- UMR 1282, Institut National de la Recherche Agronomique, Infectiologie et Santé PubliqueNouzilly, France
| | - Philippe Gérard
- UMR 1319, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Marie-Pierre Moisan
- UMR 1286, Institut National de la Recherche Agronomique, Université Bordeaux, Nutrition et Neurobiologie IntégréeBordeaux, France
| | - Léa Lansade
- PRC, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, IFCE, Université de ToursNouzilly, France
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME JOURNAL 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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Nie Y, Zhou Z, Guan J, Xia B, Luo X, Yang Y, Fu Y, Sun Q. Dynamic changes of yak ( Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:957-966. [PMID: 28183172 PMCID: PMC5495674 DOI: 10.5713/ajas.16.0836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/21/2016] [Accepted: 01/11/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. METHODS The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. RESULTS Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. CONCLUSION Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.
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Affiliation(s)
- Yuanyang Nie
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Zhiwei Zhou
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jiuqiang Guan
- Sichuan Grassland Science Academy, Chengdu, Sichuan, 611731, China
| | - Baixue Xia
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Xiaolin Luo
- Sichuan Grassland Science Academy, Chengdu, Sichuan, 611731, China
| | - Yang Yang
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Yu Fu
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Qun Sun
- Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
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Patra A, Park T, Kim M, Yu Z. Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances. J Anim Sci Biotechnol 2017; 8:13. [PMID: 28149512 PMCID: PMC5270371 DOI: 10.1186/s40104-017-0145-9] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/13/2017] [Indexed: 11/25/2022] Open
Abstract
Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane (CH4). Research on methanogens in the rumen has attracted great interest in the last decade because CH4 emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH4 emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.
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Affiliation(s)
- Amlan Patra
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA.,Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, 37 K. B. Sarani, Belgachia, Kolkata, 700037 India
| | - Tansol Park
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA
| | - Minseok Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA
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