1
|
Bax HHM, Jurak E. Characterization of Two Glycoside Hydrolases of Family GH13 and GH57, Present in a Polysaccharide Utilization Locus (PUL) of Pontibacter sp. SGAir0037. Molecules 2024; 29:2788. [PMID: 38930854 PMCID: PMC11206854 DOI: 10.3390/molecules29122788] [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: 05/23/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Glycogen, an α-glucan polymer serving as an energy storage compound in microorganisms, is synthesized through distinct pathways (GlgC-GlgA or GlgE pathway). Both pathways involve multiple enzymes, with a shared glycogen branching enzyme (GBE). GBEs play a pivotal role in establishing α-1,6-linkages within the glycogen structure. GBEs are also used for starch modification. Understanding how these enzymes work is interesting for both glycogen synthesis in microorganisms, as well as novel applications for starch modification. This study focuses on a putative enzyme GH13_9 GBE (PoGBE13), present in a polysaccharide utilization locus (PUL) of Pontibacter sp. SGAir0037, and related to the GlgE glycogen synthesis pathway. While the PUL of Pontibacter sp. SGAir0037 contains glycogen-degrading enzymes, the branching enzyme (PoGBE13) was also found due to genetic closeness. Characterization revealed that PoGBE13 functions as a typical branching enzyme, exhibiting a relatively high branching over non-branching (hydrolysis and α-1,4-transferase activity) ratio on linear maltooctadecaose (3.0 ± 0.4). Besides the GH13_9 GBE, a GH57 (PoGH57) enzyme was selected for characterization from the same PUL due to its undefined function. The combined action of both GH13 and GH57 enzymes suggested 4-α-glucanotransferase activity for PoGH57. The characterization of these unique enzymes related to a GlgE glycogen synthesis pathway provides a more profound understanding of their interactions and synergistic roles in glycogen synthesis and are potential enzymes for use in starch modification processes. Due to the structural similarity between glycogen and starch, PoGBE13 can potentially be used for starch modification with different applications, for example, in functional food ingredients.
Collapse
Affiliation(s)
| | - Edita Jurak
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands;
| |
Collapse
|
2
|
Han D, Yang Y, Guo Z, Chen K, Dai S, Zhu Y, Wang Y, Yu Z, Wang K, Liu P, Rong C, Yu Y. Metagenomics profiling of the microbial community and functional differences in solid-state fermentation vinegar starter (seed Pei) from different Chinese regions. Front Microbiol 2024; 15:1389737. [PMID: 38756727 PMCID: PMC11096547 DOI: 10.3389/fmicb.2024.1389737] [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: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction The starter used in solid-state fermentation (SSF) vinegar, known as seed Pei is a microbial inoculant from the previous batch that is utilized during the acetic acid fermentation stage. The seed Pei, which has a notable impact on vinegar fermentation and flavor, is under-researched with comparative studies on microorganisms. Methods Herein metagenomics was employed to reveal the microbes and their potential metabolic functions of four seed Pei from three regions in China. Results The predominant microbial taxa in all four starters were bacteria, followed by viruses, eukaryotes, and archaea, with Lactobacillus sp. or Acetobacter sp. as main functional taxa. The seed Pei used in Shanxi aged vinegar (SAV) and Sichuan bran vinegar (SBV) exhibited a higher similarity in microbial composition and distribution of functional genes, while those used in two Zhenjiang aromatic vinegar (ZAV) differed significantly. Redundancy analysis (RDA) of physicochemical factors and microbial communities indicated that moisture content, pH, and reducing sugar content are significant factors influencing microbial distribution. Moreover, seven metagenome-assembled genomes (MAGs) that could potentially represent novel species were identified. Conclusions There are distinctions in the microbiome and functional genes among different seed Pei. The vinegar starters were rich in genes related to carbohydrate metabolism. This research provides a new perspective on formulating vinegar fermentation starters and developing commercial fermentation agents for vinegar production.
Collapse
Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ken Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| |
Collapse
|
3
|
Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
Collapse
Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
| |
Collapse
|
4
|
Xi W, Zhang X, Zhu X, Wang J, Xue H, Pan H. Distribution patterns and influential factors of pathogenic bacteria in freshwater aquaculture sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16028-16047. [PMID: 38308166 DOI: 10.1007/s11356-024-31897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Pathogenic bacteria, the major causative agents of aquaculture diseases, are a serious impediment to the aquaculture industry. However, the bioinformatics of pathogenic bacteria and virulence factors (VFs) in sediments, an important component of freshwater aquaculture ecosystems, are not well characterized. In this study, 20 sediment samples were collected from fish pond sediments (FPS), shrimp field sediments (SFS), fish pond sediment control (FPSC), and shrimp field sediment control (SFSC). Molecular biological information was obtained on a total of 173 pathogenic bacteria, 1093 virulence factors (VFs), and 8475 mobile genetic elements (MGEs) from these samples. The results indicated that (1) aquaculture patterns and sediment characteristics can affect the distribution of pathogenic bacteria. According to the results of the Kruskal-Wallis H test, except for Mycobacterium gilvum, there were significant differences (P < 0.05) among the four sediment types in the average abundance of major pathogenic bacteria (top 30 in abundance), and the average abundance of major pathogenic bacteria in the four sediment types followed the following pattern: FPS > SFS > FPSC > SFSC. (2) Pathogenic bacteria are able to implement a variety of complex pathogenic mechanisms such as adhesion, invasion, immune evasion, and metabolic regulation in the host because they carry a variety of VFs such as type IV pili, HSI-I, Alginate, Colibactin, and Capsule. According to the primary classification of the Virulence Factor Database (VFDB), the abundance of VFs in all four types of sediments showed the following pattern: offensive VFs > non-specific VFs > defensive VFs > regulation of virulence-related genes. (3) Total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), nitrite, and nitrate were mostly only weakly positively correlated with the major pathogenic bacteria and could promote the growth of pathogenic bacteria to some extent, whereas ammonia was significantly positively correlated with most of the major pathogenic bacteria and could play an important role in promoting the growth and reproduction of pathogenic bacteria. (4) Meanwhile, there was also a significant positive correlation between CAZyme genes and major pathogenic bacteria (0.62 ≤ R ≤ 0.89, P < 0.05). This suggests that these pathogenic bacteria could be the main carriers of CAZyme genes and, to some extent, gained a higher level of metabolic activity by degrading organic matter in the sediments to maintain their competitive advantage. (5) Worryingly, the results of correlation analyses indicated that MGEs in aquaculture sediments could play an important role in the spread of VFs (R = 0.82, P < 0.01), and in particular, plasmids (R = 0.75, P < 0.01) and integrative and conjugative elements (ICEs, R = 0.65, P < 0.05) could be these major vectors of VFs. The results of this study contribute to a comprehensive understanding of the health of freshwater aquaculture sediments and provide a scientific basis for aquaculture management and conservation.
Collapse
Affiliation(s)
- Wenxiang Xi
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Xun Zhang
- China Coal Mine Construction Group Co., LTD, Hefei, 230071, Anhui, China
| | - Xianbin Zhu
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Jiaming Wang
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Han Xue
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Hongzhong Pan
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China.
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China.
| |
Collapse
|
5
|
Ma X, La Y, Yang G, Dai R, Zhang J, Zhang Y, Jin J, Ma X, Guo X, Chu M, Yan P, Zhang Q, Liang C. Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions. Front Microbiol 2024; 14:1309535. [PMID: 38264487 PMCID: PMC10803511 DOI: 10.3389/fmicb.2023.1309535] [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: 10/08/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.
Collapse
Affiliation(s)
- Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Guowu Yang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Juanxiang Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yonghui Zhang
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Jiaming Jin
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qiang Zhang
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, Lhasa, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| |
Collapse
|
6
|
Hu X, Gu H, Sun X, Wang Y, Liu J, Yu Z, Li Y, Jin J, Wang G. Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation. CHEMOSPHERE 2024; 348:140762. [PMID: 38006912 DOI: 10.1016/j.chemosphere.2023.140762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/08/2023] [Accepted: 11/17/2023] [Indexed: 11/27/2023]
Abstract
Agricultural mulch films are frequently applied to achieve high yield, resulting in large quantities of microplastic (MP) pollution in agroecosystem. However, studies focusing specifically on the diversity of MP-degrading enzymes and related microbial communities have yet to be conducted. Here, we established a soil microcosmic incubation with addition of 5% (w/w) conventional (low-density polyethylene (LDPE)) and biodegradable (blend of polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) MPs for incubation 90 days. The DNA samples extracted from soils and plastisphere of MPs were examined by metagenomics and genome binning methods, specifically targeting carbohydrate-active enzymes (CAZymes) and plastic-degrading enzymes (PDZymes). The results revealed that plastisphere of MPs exhibited significantly distinct patterns of CAZymes and PDZymes from soils, and abundances of all examined exoenzymes were higher in plastisphere than those in soils. Plastisphere of LDPE-MPs selectively enriched proteases and alkane monooxygenase (alkB), and required families of carbohydrate-binding module (CBM) to increase the binding of CAZymes with MPs. Dissimilarly, diverse CAZymes with high abundances were observed in the plastisphere of PBAT-PLA MPs and esterases were important indicative PDZymes for PBAT-PLA degradation. The enriched exoenzymes in plastisphere of LDPE-MPs were mainly assigned to Actinobacteria while Proteobacteria with higher abundance in plastisphere of PBAT-PLA MPs containing most indicative exoenzymes. Moreover, a high-quality genome classified as Amycolatopsis japonica was reconstructed and found to contain one or more gene copies of indicative exoenzymes for polyethylene. Two novel genomes classified as Sphingomonas were selectively enriched in plastisphere of PBAT-PLA MPs and contained diverse genes encoding degrading exoenzymes. Taken together, our study highlighted the CAZymes and PDZymes can be exploited as potent microbial strategies for solving MPs pollution in croplands.
Collapse
Affiliation(s)
- Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongbin Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| |
Collapse
|
7
|
Zhu J, Song Y, Xiao Y, Ma L, Hu C, Yang H, Wang X, Lyu W. Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese. Br Poult Sci 2023; 64:565-576. [PMID: 37493577 DOI: 10.1080/00071668.2023.2239172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023]
Abstract
1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.
Collapse
Affiliation(s)
- J Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Y Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Y Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - L Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - C Hu
- College of Animal Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - H Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - X Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - W Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
8
|
Jiang H, Cao HW, Chai ZX, Chen XY, Zhang CF, Zhu Y, Xin JW. Dynamic alterations in yak ( Bos grunniens) rumen microbiome in response to seasonal variations in diet. Physiol Genomics 2022; 54:514-525. [PMID: 36342051 DOI: 10.1152/physiolgenomics.00112.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.
Collapse
Affiliation(s)
- Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Xiao-Ying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, People's Republic of China.,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| |
Collapse
|
9
|
Yan Z, Kang E, Zhang K, Hao Y, Wang X, Li Y, Li M, Wu H, Zhang X, Yan L, Zhang W, Li J, Yang A, Niu Y, Kang X. Asynchronous responses of microbial CAZymes genes and the net CO 2 exchange in alpine peatland following 5 years of continuous extreme drought events. ISME COMMUNICATIONS 2022; 2:115. [PMID: 37938678 PMCID: PMC9723601 DOI: 10.1038/s43705-022-00200-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2023]
Abstract
Peatlands act as an important sink of carbon dioxide (CO2). Yet, they are highly sensitive to climate change, especially to extreme drought. The changes in the net ecosystem CO2 exchange (NEE) under extreme drought events, and the driving function of microbial enzymatic genes involved in soil organic matter (SOM) decomposition, are still unclear. Herein we investigated the effects of extreme drought events in different periods of plant growth season at Zoige peatland on NEE and microbial enzymatic genes of SOM decomposition after 5 years. The results showed that the NEE of peatland decreased significantly by 48% and 26% on average (n = 12, P < 0.05) under the early and midterm extreme drought, respectively. The microbial enzymatic genes abundance of SOM decomposition showed the same decreasing trend under early and midterm extreme drought, but an increasing trend under late extreme drought. The microbial community that contributes to these degradation genes mainly derives from Proteobacteria and Actinobacteria. NEE was mainly affected by soil hydrothermal factors and gross primary productivity but weakly correlated with SOM enzymatic decomposition genes. Soil microbial respiration showed a positive correlation with microbial enzymatic genes involved in the decomposition of labile carbon (n = 18, P < 0.05). This study provided new insights into the responses of the microbial decomposition potential of SOM and ecosystem CO2 sink function to extreme drought events in the alpine peatland.
Collapse
Affiliation(s)
- Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Enze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaodong Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Haidong Wu
- Information Center of Ministry of Ecology and Environment, 100029, Beijing, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Wantong Zhang
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China.
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China.
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China.
| |
Collapse
|
10
|
Venturini AM, Gontijo JB, Mandro JA, Paula FS, Yoshiura CA, da França AG, Tsai SM. Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils. Microb Genom 2022; 8. [PMID: 35894927 PMCID: PMC9455692 DOI: 10.1099/mgen.0.000853] [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] [Indexed: 12/28/2022] Open
Abstract
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
Collapse
Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| |
Collapse
|
11
|
Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential. 3 Biotech 2022; 12:132. [PMID: 35611093 DOI: 10.1007/s13205-022-03190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/26/2022] [Indexed: 11/01/2022] Open
Abstract
Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03190-7.
Collapse
|
12
|
Kallscheuer N, Jogler C. The bacterial phylum Planctomycetes as novel source for bioactive small molecules. Biotechnol Adv 2021; 53:107818. [PMID: 34537319 DOI: 10.1016/j.biotechadv.2021.107818] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.
Collapse
Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| |
Collapse
|
13
|
Piel T, Sandrini G, Muyzer G, Brussaard CPD, Slot PC, van Herk MJ, Huisman J, Visser PM. Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms. Microorganisms 2021; 9:microorganisms9071495. [PMID: 34361929 PMCID: PMC8304526 DOI: 10.3390/microorganisms9071495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022] Open
Abstract
Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.
Collapse
Affiliation(s)
- Tim Piel
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Giovanni Sandrini
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Corina P. D. Brussaard
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands
| | - Pieter C. Slot
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Maria J. van Herk
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Petra M. Visser
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Correspondence: ; Tel.: +31-20-5257073
| |
Collapse
|
14
|
New Insights into the Co-Occurrences of Glycoside Hydrolase Genes among Prokaryotic Genomes through Network Analysis. Microorganisms 2021; 9:microorganisms9020427. [PMID: 33669523 PMCID: PMC7922503 DOI: 10.3390/microorganisms9020427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/21/2022] Open
Abstract
Glycoside hydrolase (GH) represents a crucial category of enzymes for carbohydrate utilization in most organisms. A series of glycoside hydrolase families (GHFs) have been classified, with relevant information deposited in the CAZy database. Statistical analysis indicated that most GHFs (134 out of 154) were prone to exist in bacteria rather than archaea, in terms of both occurrence frequencies and average gene numbers. Co-occurrence analysis suggested the existence of strong or moderate-strong correlations among 63 GHFs. A combination of network analysis by Gephi and functional classification among these GHFs demonstrated the presence of 12 functional categories (from group A to L), with which the corresponding microbial collections were subsequently labeled, respectively. Interestingly, a progressive enrichment of particular GHFs was found among several types of microbes, and type-L as well as type-E microbes were deemed as functional intensified species which formed during the microbial evolution process toward efficient decomposition of lignocellulose as well as pectin, respectively. Overall, integrating network analysis and enzymatic functional classification, we were able to provide a new angle of view for GHs from known prokaryotic genomes, and thus this study is likely to guide the selection of GHs and microbes for efficient biomass utilization.
Collapse
|
15
|
dos Santos Melo-Nascimento AO, Mota Moitinho Sant´Anna B, Gonçalves CC, Santos G, Noronha E, Parachin N, de Abreu Roque MR, Bruce T. Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1. PLoS One 2020; 15:e0243739. [PMID: 33351813 PMCID: PMC7755216 DOI: 10.1371/journal.pone.0243739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.
Collapse
Affiliation(s)
| | | | - Carolyne Caetano Gonçalves
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Giovanna Santos
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Eliane Noronha
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Nádia Parachin
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Milton Ricardo de Abreu Roque
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Instituto de Ciências da Saúde, Laboratório de Bioprospecção, Universidade Federal da Bahia, Salvador, Brazil
| | - Thiago Bruce
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
- * E-mail:
| |
Collapse
|
16
|
Grieco MB, Lopes FAC, Oliveira LS, Tschoeke DA, Popov CC, Thompson CC, Gonçalves LC, Constantino R, Martins OB, Kruger RH, de Souza W, Thompson FL. Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Curr Microbiol 2019; 76:687-697. [DOI: 10.1007/s00284-019-01662-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/22/2019] [Indexed: 01/04/2023]
|
17
|
Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater. Arch Microbiol 2018; 200:1267-1278. [PMID: 29947838 DOI: 10.1007/s00203-018-1532-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/16/2018] [Accepted: 05/26/2018] [Indexed: 10/14/2022]
Abstract
Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.
Collapse
|