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Yang T, Wang Y, Zhou T, Yang J, Liu M, Shang Y, Zhang Y, Hei P. Modeling microbial impact on macrophyte debris decomposition in macrophyte-dominated eutrophic lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174442. [PMID: 38964387 DOI: 10.1016/j.scitotenv.2024.174442] [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: 03/05/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The decomposition of macrophytes plays a crucial role in the nutrient cycles of macrophyte-dominated eutrophication lakes. While research on plant decomposition mechanisms and microbial influences has rapid developed, it is curious that plant decomposition models have remained stagnant at the single-stage model from 50 years ago, without endeavor to consider any important factors. Our research conducted in-situ experiments and identified the optimal metrics for decomposition-related microbes, thereby establishing models for microbial impacts on decomposition rates (k_RDR). Using backward elimination in stepwise regression, we found that the optimal subset of independent variables-specifically Gammaproteobacteria-Q-L, Actinobacteriota-Q-L, and Ascomycota-Q-L-increased the adjusted R-squared (Ra2) to 0.93, providing the best modeling for decomposition rate (p = 0.002). Additionally, k_RDR can be modeled by synergic parameters of ACHB-Q-L, LDB-Q-L, and AB-Q-L for bacteria, and SFQ for fungi, albeit with a slightly lower Ra2 of 0.7-0.9 (p < 0.01). The primary contribution of our research lies in two key aspects. Firstly, we introduced optimal metrics for modeling microbes, opting for debris surface microbes over sediment microbes, and prioritizing absolute abundance over relative abundance. Secondly, our model represents a noteworthy advancement in debris modeling. Alongside elucidating the focus and innovative aspects of our work, we also addressed existing limitations and proposed directions for future research. SYNOPSIS: This study explores optimum metrics for decomposition-related microbes, offering precise microbial models for enhanced lake nutrient cycle simulation.
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Affiliation(s)
- Tingting Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yaqin Wang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Tong Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Jing Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Manman Liu
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yizi Shang
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yingyuan Zhang
- Guizhou Academy of Testing and Analysis, Guiyang 550000, China
| | - Pengfei Hei
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China.
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Zhang P, Zhang H, Li Y, Zhang J, Ma C, Weng N, Gao X, Wu F, Huo S. Strong associations between dissolved organic matter and microbial communities in the sediments of Qinghai-Tibetan Plateau lakes depend on salinity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171857. [PMID: 38521264 DOI: 10.1016/j.scitotenv.2024.171857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
In aquatic ecosystems, dissolved organic matter (DOM) plays a vital role in microbial communities and the biogeochemical cycling of elements. However, little is known about the associations between DOM and microbial communities in lake sediments. This study investigated the composition of water-extractable organic matter and microbial communities in surface sediments of lakes with different salinities on the Qinghai-Tibet Plateau. Ultrahigh-resolution mass spectrometry and high-throughput microbial sequencing techniques were employed to assess the associations between molecular diversity and microbial diversity and the effects of salinity in 19 lakes spanning a salinity range from 0.22 ‰ to 341.87 ‰. Our results show that increasing salinity of lake water led to higher molecular diversity of DOM in surface sediments. High-salinity lakes exhibited distinct DOM characteristics, such as lower aromaticity, smaller molecular weight, and higher oxidation degree, compared to freshwater lakes. The complexity of the microbial network composition of sediments first increased and then decreased with the increase of salinity. Moreover, as salinity increases, the dominant species transitioned from Gammaproteobacteria to Bacteroidia, and this transition was accompanied by a decrease in microbial diversity and an increase in molecular diversity. Microbial factors accounted for 34.68 % of the variation in the molecular composition of DOM. Overall, this study emphasizes the significant effects of salinity on both molecular and microbial diversity in lake sediments. Furthermore, our findings underscore the importance of microbes in controlling the range of organic compounds present in lakes and deepen our knowledge of the biogeochemical cycling of DOM.
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Affiliation(s)
- Peilian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jingtian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Chunzi Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xing Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Zhao S, Liu X, Banerjee S, Hartmann M, Peng B, Elvers R, Zhao ZY, Zhou N, Liu JJ, Wang B, Tian CY, Jiang J, Lian TX. Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil. Appl Environ Microbiol 2024; 90:e0235523. [PMID: 38535171 PMCID: PMC11022556 DOI: 10.1128/aem.02355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/04/2024] [Indexed: 04/18/2024] Open
Abstract
Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xu Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Bin Peng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Rylie Elvers
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Zhen-Yong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Na Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Jun-Jie Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Chang-Yan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Teng-Xiang Lian
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
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Liu X, Salles JF. Lose-lose consequences of bacterial community-driven invasions in soil. MICROBIOME 2024; 12:57. [PMID: 38494494 PMCID: PMC10946201 DOI: 10.1186/s40168-024-01763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities. RESULTS Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community. CONCLUSIONS Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.
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Affiliation(s)
- Xipeng Liu
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG, Groningen, The Netherlands.
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Swathy K, Vivekanandhan P, Yuvaraj A, Sarayut P, Kim JS, Krutmuang P. Biodegradation of pesticide in agricultural soil employing entomopathogenic fungi: Current state of the art and future perspectives. Heliyon 2024; 10:e23406. [PMID: 38187317 PMCID: PMC10770572 DOI: 10.1016/j.heliyon.2023.e23406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Pesticides play a pivotal role in agriculture for the effective production of various crops. The indiscriminate use of pesticides results in the significant bioaccumulation of pesticide residues in vegetables. This situation is beyond the control of consumers and poses a serious health issue for human beings. Occupational exposure to pesticides may occur for farmers, agricultural workers, and industrial producers of pesticides. This occupational exposure primarily causes food and water contamination that gets into humans and environmental pollution. Depending on the toxicity of pesticides, the causes and effects differ in the environment and in human health. The number of criteria used and the method of implementation employed to assess the effect of pesticides on humans and the environment have been increasing, as they may provide characterization of pesticides that are already on the market as well as those that are on the way. The biological control of pests has been increasing nowadays to combat all these effects caused by synthetic pesticides. Myco-biocontrol has received great attention in research because it has no negative impact on humans, the environment, or non-target species. Entomopathogenic fungi are microbes that have the ability to kill insect pests. Fungi also make enzymes like the lytic enzymes, esterase, oxidoreductase, and cytochrome P450, which react with chemical residues in the field and break them down into nontoxic substances. In this review, the authors looked at how entomopathogenic fungi break down insecticides in the environment and how their enzymes break down insecticides on farms.
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Affiliation(s)
- Kannan Swathy
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Perumal Vivekanandhan
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of General Pathology at Saveetha Dental College and Hospitals in the Saveetha Institute of Medical & Technical Sciences at Saveetha University in Chennai, Tamil Nadu, 600077, India
| | | | - Pittarate Sarayut
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jae Su Kim
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, South Korea
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Patcharin Krutmuang
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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Ma W, Lin L, Peng Q. Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates. MICROBIAL ECOLOGY 2023; 86:1589-1603. [PMID: 36717391 DOI: 10.1007/s00248-023-02170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.
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Affiliation(s)
- Wenwen Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
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Zhang Y, Yang K, Chen H, Dong Y, Li W. Origin, composition, and accumulation of dissolved organic matter in a hypersaline lake of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161612. [PMID: 36642270 DOI: 10.1016/j.scitotenv.2023.161612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Inland saline lakes are widely distributed and commonly exist in arid and semi-arid regions. Dissolved organic matter (DOM) in saline lakes plays an important role in the global carbon cycle and is a key regulator of saline lake ecosystem functions through biotic and abiotic processes. However, the origin, composition, and cycling of DOM in saline lakes, especially hypersaline lakes, remain largely unknown. In this study, two lake brine DOM samples and three input river DOM samples from a hypersaline lake, Da Qaidam Lake (DQL) in the Qaidam Basin of the Qinghai-Tibet Plateau (QTP), were isolated and analyzed using a multi-analytical approach. The results indicated that, although terrestrial in origin, the DOM composition and features of DQL were dominated by indigenous in-lake processes owing to the very long water residence time of the lake brine. Lake DOM contained more aliphatic compounds but fewer aromatic compounds than DOM from the rivers. Lake DOM also exhibited more chemodiversity and contained highly saturated and oxidized components that were incorporated with heteroatoms. Despite the limited contributions from riverine DOM, some special features of lake DOM, such as the high content of sulfur-bearing components, may be partly related to the long-term accumulation of hotspring riverine input. Flocculation, photodegradation, microbial degradation, evapo-concentration, and primary production processes were considered synergistic factors in the persistence and features of the hypersaline lake DOM. The results of this study can further our knowledge of the transformation and long-term turnover of DOM in hypersaline lakes and how DOM chemodiversity changes across wide aquatic ecosystems.
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Affiliation(s)
- Yaoling Zhang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, PR China; Qinghai Provincial Key Laboratory of Resources and Chemistry of Salt Lakes, Xining 810008, PR China.
| | - Keli Yang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, PR China; Qinghai Technology Research and Development Center of Comprehensive Utilization of Salt Lake Resources, Xining 810008, PR China
| | - Hongmei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, PR China
| | - Yaping Dong
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, PR China; Qinghai Technology Research and Development Center of Comprehensive Utilization of Salt Lake Resources, Xining 810008, PR China
| | - Wu Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, PR China; Qinghai Provincial Key Laboratory of Resources and Chemistry of Salt Lakes, Xining 810008, PR China.
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Lafuente E, Carles L, Walser J, Giulio M, Wullschleger S, Stamm C, Räsänen K. Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore ( Asellus aquaticus). Evol Appl 2023; 16:824-848. [PMID: 37124094 PMCID: PMC10130563 DOI: 10.1111/eva.13540] [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: 09/05/2022] [Revised: 01/24/2023] [Accepted: 02/17/2023] [Indexed: 04/03/2023] Open
Abstract
Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.
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Affiliation(s)
- Elvira Lafuente
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Louis Carles
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Jean‐Claude Walser
- Department of Environmental Systems Science D‐USYS, Genetic Diversity CentreSwiss Federal Institute of Technology (ETH), ZürichZürichSwitzerland
| | - Marco Giulio
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Simon Wullschleger
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Christian Stamm
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Katja Räsänen
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Wu Z, Peng K, Zhang Y, Wang M, Yong C, Chen L, Qu P, Huang H, Sun E, Pan M. Lignocellulose dissociation with biological pretreatment towards the biochemical platform: A review. Mater Today Bio 2022; 16:100445. [PMID: 36212906 PMCID: PMC9535326 DOI: 10.1016/j.mtbio.2022.100445] [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: 07/20/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
Abstract
Lignocellulose utilization has been gaining great attention worldwide due to its abundance, accessibility, renewability and recyclability. Destruction and dissociation of the cross-linked, hierarchical structure within cellulose hemicellulose and lignin is the key procedure during chemical utilization of lignocellulose. Of the pretreatments, biological treatment, which can effectively target the complex structures, is attractive due to its mild reaction conditions and environmentally friendly characteristics. Herein, we report a comprehensive review of the current biological pretreatments for lignocellulose dissociation and their corresponding degradation mechanisms. Firstly, we analyze the layered, hierarchical structure of cell wall, and the cross-linked network between cellulose, hemicellulose and lignin, then highlight that the cracking of β-aryl ether is considered the key to lignin degradation because of its dominant position. Secondly, we explore the effect of biological pretreatments, such as fungi, bacteria, microbial consortium, and enzymes, on substrate structure and degradation efficiency. Additionally, combining biological pretreatment with other methods (chemical methods and catalytic materials) may reduce the time necessary for the whole process, which also help to strengthen the lignocellulose dissociation efficiency. Thirdly, we summarize the related applications of lignocellulose, such as fuel production, chemicals platform, and bio-pulping, which could effectively alleviate the energy pressure through bioconversion into high value-added products. Based on reviewing of current progress of lignocellulose pretreatment, the challenges and future prospects are emphasized. Genetic engineering and other technologies to modify strains or enzymes for improved biotransformation efficiency will be the focus of future research.
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Affiliation(s)
- Zengyou Wu
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kun Peng
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yin Zhang
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Mei Wang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Cheng Yong
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ling Chen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ping Qu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hongying Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Enhui Sun
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
- College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa
- Corresponding author. Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Mingzhu Pan
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Corresponding author.
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11
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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12
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Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential. Microorganisms 2022; 10:microorganisms10112230. [PMID: 36422301 PMCID: PMC9692603 DOI: 10.3390/microorganisms10112230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.
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13
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Zhu J, Liu J, Li W, Ru Y, Sun D, Liu C, Li Z, Liu W. Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose. BIORESOUR BIOPROCESS 2022; 9:110. [PMID: 38647799 PMCID: PMC10991580 DOI: 10.1186/s40643-022-00601-8] [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: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.
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Affiliation(s)
- Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Weilin Li
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunrui Ru
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
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14
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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15
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Agarase, Amylase and Xylanase from Halomonas meridiana: A Study on Optimization of Coproduction for Biomass Saccharification. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coproduction of multienzymes from single potential microbe has captivated contemplation in industries. Bacterial strain, Halomonas meridiana VITSVRP14, isolated from seaweed was labored to produce amylase, agarase and xylanase conjointly using submerged fermentation. The optimum production conditions clinched by classical optimization were: pH 8; 1.5% inoculum; 24 h incubation, 40 °C; 8% NaCl (sodium chloride); 1% lactose and NaNO3 (sodium nitrate). The preponderant variables (pH, temperature, lactose) and their interaction effect on enzyme production were studied by Plackett-Burman design and Response Surface Methodology (RSM). There were 3.29, 1.81 and 2.08 fold increase in enzyme activity with respect to agarase, amylase and xylanase after optimization against basal medium. After 24 h of enzymatic treatment, the saccharification rates of the coproduced enzyme mixture were 38.96% on rice bran, 49.85% on wheat bran, 61.2% on cassava bagasse and 57.82% on corn cob. Thus, the coproduced enzyme mixture from a bacterium with halotolerance is plausible in pretreated lignocellulose degradation. The ability of this single microbe Halomonas meridiana VITSVRP14, in coproducing agarase, amylase and xylanase give the nod for its application in biomass saccharification by subsiding cost, energy and time involved in the process.
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16
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Yang X, Shang G, Wang X. Biochemical, transcriptomic, gut microbiome responses and defense mechanisms of the earthworm Eisenia fetida to salt stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113684. [PMID: 35623149 DOI: 10.1016/j.ecoenv.2022.113684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/05/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
The accumulation of sodium chloride (NaCl) in soil is a worldwide problem with detrimental effects on the survival of soil animals. The effects of NaCl on earthworms remain unclear. Here, we show that the growth rate, cocoon production rate, annetocin precursor (ANN) mRNA level, and superoxide dismutase and catalase activities in earthworms were reduced under NaCl stress, whereas the mortality rate, reactive oxygen species (ROS) and malondialdehyde activity level increased. Histological damage to the earthworm body wall and intestine were observed under NaCl stress. NaCl stress increased DNA damage in the seminal vesicle and coelomocytes. The mRNA level of lumbrokinase, 1,3-beta-glucanse, coelomic cytolytic factor (CCF1), and alpha-amylase was significantly down-regulated, whereas that of earthworm excitatory peptides2 (EEP2) was up-regulated. From 16 S rRNA sequencing, the earthworm gut microbiota diversity decreased under NaCl stress. However, Verminephrobacter, Kluyvera, Lactobacillus, and Ochrobactrum increased under NaCl stress. These findings contribute to the risk assessment of the salt stress on soil organisms.
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Affiliation(s)
- Xuelian Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou 215128, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing 100193, China
| | - Guangshen Shang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xing Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing 100193, China.
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17
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Dutta B, Bandopadhyay R. Biotechnological potentials of halophilic microorganisms and their impact on mankind. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:75. [PMID: 35669848 PMCID: PMC9152817 DOI: 10.1186/s43088-022-00252-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Halophiles are extremophilic organisms represented by archaea, bacteria and eukaryotes that thrive in hypersaline environment. They apply different osmoadaptation strategies to survive in hostile conditions. Habitat diversity of halophilic microorganisms in hypersaline system provides information pertaining the evolution of life on Earth. Main body The microbiome-gut-brain axis interaction contributes greatly to the neurodegenerative diseases. Gut resident halophilic bacteria are used as alternative medication for chronic brain diseases. Halophiles can be used in pharmaceuticals, drug delivery, agriculture, saline waste water treatment, biodegradable plastic production, metal recovery, biofuel energy generation, concrete crack repair and other sectors. Furthermore, versatile biomolecules, mainly enzymes characterized by broad range of pH and thermostability, are suitable candidate for industrial purposes. Reflectance pattern of halophilic archaeal pigment rhodopsin is considered as potential biosignature for Earth-like planets. Short conclusions This review represents important osmoadaptation strategies acquired by halophilic archaea and bacteria and their potential biotechnological applications to resolve present day challenges. Graphical Abstract
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Affiliation(s)
- Bhramar Dutta
- Department of Botany, The University of Burdwan, Purba Bardhaman, West Bengal 713104 India
| | - Rajib Bandopadhyay
- Department of Botany, The University of Burdwan, Purba Bardhaman, West Bengal 713104 India
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18
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Rinke M, Maraun M, Scheu S. Spatial and temporal variations in salt marsh microorganisms of the Wadden Sea. Ecol Evol 2022; 12:e8767. [PMID: 35356561 PMCID: PMC8958242 DOI: 10.1002/ece3.8767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 12/05/2022] Open
Abstract
Salt marshes exist at the interface of the marine and the terrestrial system. Shore height differences and associated variations in inundation frequency result in altered abiotic conditions, plant communities, and resource input into the belowground system. These factors result in three unique zones, the upper salt marsh (USM), the lower salt marsh (LSM), and the pioneer zone (PZ). Marine detritus, such as micro- and macroalgae, is typically flushed into the PZ daily, with storm surges moving both salt marsh detritus and marine detritus into higher salt marsh zones. Microbial assemblages are essential for the decomposition of organic matter and have been shown to sensitively respond to changes in abiotic conditions such as oxygen supply and salinity. However, temporal and spatial dynamics of microbial communities of Wadden Sea salt marshes received little attention. We investigated the dynamics of soil microbial communities across horizontal (USM, LSM, and PZ), vertical (0-5 and 5-10-cm sediment depth), and temporal (spring, summer, and autumn) scales in the Wadden Sea salt marsh of the European North Atlantic coast using phospholipid fatty acid (PLFA) analysis. Our results show strong spatial dynamics both among salt marsh zones and between sediment depths, but temporal dynamics to be only minor. Despite varying in space and time, PLFA markers indicated that bacteria generally were the dominant microbial group across salt marsh zones and seasons, however, their dominance was most pronounced in the USM, whereas fungal biomass peaked in the LSM and algal biomass in the PZ. Only algal markers and the stress marker monounsaturated to saturated fatty acid ratio responded to seasonality. Overall, therefore, the results indicate remarkable temporal stability of salt marsh microbial communities despite strong variability in abiotic factors.
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Affiliation(s)
- Maria Rinke
- J.F. Blumenbach Institute of Zoology and Anthropology, Animal EcologyUniversity of GöttingenGöttingenGermany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology, Animal EcologyUniversity of GöttingenGöttingenGermany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Animal EcologyUniversity of GöttingenGöttingenGermany
- Centre of Biodiversity and Sustainable Land UseUniversity of GöttingenGöttingenGermany
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19
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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20
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Suman J, Strejcek M, Zubrova A, Capek J, Wald J, Michalikova K, Hradilova M, Sredlova K, Semerad J, Cajthaml T, Uhlik O. Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone. Front Microbiol 2021; 12:644708. [PMID: 34721309 PMCID: PMC8552027 DOI: 10.3389/fmicb.2021.644708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, the diversity of bphA genes was assessed in a 13C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with 13C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jan Capek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Wald
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Klara Michalikova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Miluse Hradilova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Kamila Sredlova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Jaroslav Semerad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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21
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Banu JR, Kumar G, Chattopadhyay I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 2021; 11:429. [PMID: 34603908 DOI: 10.1007/s13205-021-02962-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
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Affiliation(s)
- J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
| | - Gopalakrishnan Kumar
- Faculty of Science and Technology, Institute of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Forus, Box 8600, 4036 Stavanger, Norway
| | - Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
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22
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Bánfi R, Pohner Z, Szabó A, Herczeg G, Kovács GM, Nagy A, Márialigeti K, Vajna B. Succession and potential role of bacterial communities during Pleurotus ostreatus production. FEMS Microbiol Ecol 2021; 97:fiab125. [PMID: 34498665 PMCID: PMC8445668 DOI: 10.1093/femsec/fiab125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
There is an increasing interest in studying bacterial-fungal interactions (BFIs), also the interactions of Pleurotus ostreatus, a model white-rot fungus and important cultivated mushroom. In Europe, P. ostreatus is produced on a wheat straw-based substrate with a characteristic bacterial community, where P. ostreatus is exposed to the microbiome during substrate colonisation. This study investigated how the bacterial community structure was affected by the introduction of P. ostreatus into the mature substrate. Based on the results obtained, the effect of the presence and absence of this microbiome on P. ostreatus production in an experimental cultivation setup was determined. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and amplicon sequencing revealed a definite succession of the microbiome during substrate colonisation and fruiting body production: a sharp decrease in relative abundance of Thermus spp. and Actinobacteria, and the increasing dominance of Bacillales and Halomonas spp. The introduced experimental cultivation setup proved the protective role of the microbial community against competing fungi without affecting P. ostreatus growth. We could also demonstrate that this effect could be attributed to both living microbes and their secreted metabolites. These findings highlight the importance of bacterial-fungal interactions during mushroom production.
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Affiliation(s)
- Renáta Bánfi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Zsuzsanna Pohner
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Adrienn Nagy
- Pilze-Nagy Ltd., Talfája 50., H-6000 Kecskemét, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
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23
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Pérez-Hernández V, Hernández-Guzmán M, Luna-Guido M, Navarro-Noya YE, Romero-Tepal EM, Dendooven L. Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction. Microorganisms 2021; 9:1297. [PMID: 34203640 PMCID: PMC8232260 DOI: 10.3390/microorganisms9061297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022] Open
Abstract
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.
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Affiliation(s)
- Valentín Pérez-Hernández
- Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla Gutiérrez, Chiapas 29050, Mexico;
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Mario Hernández-Guzmán
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Marco Luna-Guido
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Yendi E. Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala 90070, Mexico;
| | - Elda M. Romero-Tepal
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6001. [PMID: 34204975 PMCID: PMC8199887 DOI: 10.3390/ijerph18116001] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
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Affiliation(s)
| | - Mohd Rafatullah
- Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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25
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Du R, Li C, Pan P, Sze Ki Lin C, Yan J. Characterization and evaluation of a natural derived bacterial consortium for efficient lignocellulosic biomass valorization. BIORESOURCE TECHNOLOGY 2021; 329:124909. [PMID: 33684842 DOI: 10.1016/j.biortech.2021.124909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Abstract
A consortium (HPP) with improved ability in biomass conversion was achieved by adjusting the proportion of Pseudoxanthomonas taiwanensis in a natural consortium (HP), but the mechanism behind was unknown. Herein, the diversities of microbial community structure and gene functions of the consortia were analyzed first, and found that HPP had a more balanced microbial structure with enriched gene pathways related to cellular processes, environmental information processing and metabolism. Then, key genes responsible for biomass conversion were further analyzed, finding that their abundance and distribution contributed to HPP's efficient biomass conversion. Finally, consolidated bioprocessing of agricultural wastes by HPP was carried out to verify its enhanced ability, and ethanol with the highest yield that was ever reported was achieved at 0.28 g/g. This is the first study which reported the underlying mechanisms for synergistic effects of microbial consortia, and will guide the artificial construction of complex microbial consortium for specific purpose.
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Affiliation(s)
- Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peipei Pan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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26
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Zoia L, Salanti A, Giorgione C, Gentili R, Citterio S, Gandolfi I, Franzetti A, Orlandi M. Integrated biological and chemical characterisation of a pair of leonardesque canal lock gates. PLoS One 2021; 16:e0247478. [PMID: 33690726 PMCID: PMC7946225 DOI: 10.1371/journal.pone.0247478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Abstract
The Museo Nazionale della Scienza e della Tecnologia “Leonardo da Vinci” in Milan is exposing two pairs of canal lock gates, used to control the water flow in Milan canal system, whose design appears in the Leonardo’s Codex Atlanticus. The wood present in the gates has been deeply characterised by mean of a multidisciplinary investigation involving i) DNA barcoding of wood fragments; ii) microbial community characterisation, and iii) chemical analyses. DNA barcoding revealed that two fragments of the gates belonged to wood species widely used in the middle age: Fagus sylvatica and Picea abies. The chemical characterisations were based on the use of ionic liquid as dissolving medium in order to analyse the entire cell wall material by means of Gel Permeation Chromatography (GPC) and 2D-NMR-HSQC techniques. This multidisciplinary analytical approach was able to highlight the complex nature of the degradation occurred during the gate operation (XVI-XVIII centuries): an intricate interplay between microbial populations (i.e. Shewanella), inorganic factors (i.e. iron from nails), physical factors and the lignocellulosic material.
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Affiliation(s)
- Luca Zoia
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
- * E-mail:
| | - Anika Salanti
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Claudio Giorgione
- Museo Nazionale della Scienza e della Tecnologia “Leonardo da Vinci”, Milano, Italy
| | - Rodolfo Gentili
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Sandra Citterio
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Marco Orlandi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
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27
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Leadbeater DR, Oates NC, Bennett JP, Li Y, Dowle AA, Taylor JD, Alponti JS, Setchfield AT, Alessi AM, Helgason T, McQueen-Mason SJ, Bruce NC. Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. MICROBIOME 2021; 9:48. [PMID: 33597033 PMCID: PMC7890819 DOI: 10.1186/s40168-020-00964-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/06/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. RESULTS Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. CONCLUSIONS Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments. Video Abstract.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joe D Taylor
- School of Chemistry and Biosciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Juliana Sanchez Alponti
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Alexander T Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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28
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Gavande PV, Basak A, Sen S, Lepcha K, Murmu N, Rai V, Mazumdar D, Saha SP, Das V, Ghosh S. Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization. Sci Rep 2021; 11:3032. [PMID: 33542396 PMCID: PMC7862241 DOI: 10.1038/s41598-021-82163-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Rice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g-1 rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.
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Affiliation(s)
- Parmeshwar V. Gavande
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Arijita Basak
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Subhajit Sen
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Khusboo Lepcha
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Nensina Murmu
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Vijeta Rai
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Deepika Mazumdar
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Vaskar Das
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Shilpi Ghosh
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
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Yang J, Jiang H, Liu W, Huang L, Huang J, Wang B, Dong H, Chu RK, Tolic N. Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes. ISME JOURNAL 2020; 14:2313-2324. [PMID: 32483305 PMCID: PMC7608266 DOI: 10.1038/s41396-020-0689-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli, Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China. .,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, China.
| | - Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China. .,Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nikola Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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30
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Liu Y, Cheng D, Xue J, Weaver L, Wakelin SA, Feng Y, Li Z. Changes in microbial community structure during pig manure composting and its relationship to the fate of antibiotics and antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:122082. [PMID: 32004835 DOI: 10.1016/j.jhazmat.2020.122082] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/30/2019] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
Animal manure containing veterinary antibiotics is a significant source of microbial antibiotic resistance genes (ARGs). Composting of animal manure with wheat straw and sawdust was explored as a means to reduce ARGs load in the final material. The effects of ciprofloxacin, oxytetracycline, sulfamerazine on the bacterial community composition, and how this then affected the removal of seven tetracycline resistance genes (TARGs), four sulfonamide resistance genes (SARGs), and two fluoroquinolone resistance genes (QARGs) were investigated. Treatments receiving either ciprofloxacin or the three mixed antibiotics had reduced bacterial alpha-diversity and displayed shifts in the abundance of Proteobacteria and Firmicutes. This demonstrated that different antibiotics played an important role in bacterial community composition. Furthermore, variation in the physicochemical properties of compost, particularly pH and temperature, was also strongly linked to shifts in bacterial composition over time. Based on network analysis, the reduction of TARGs were associated with loss of Pseudomonas, Pseudoxanthomonas, Pusillimonas, Aquamicrobium, Ureibacillus, Lysinibacillus, Bacillus and Brachybacterium during the thermophilic stage. However, QARGs and SARGs were more strongly affected by the presence of multiple antibiotics. Our results have important implications for reducing the spread of certain ARGs by controlling the composting temperature, pH or the antibiotics species used in husbandry.
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Affiliation(s)
- Yuanwang Liu
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; Scion, Private Bag 29237, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand
| | | | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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31
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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Yang Y, Liu X, Cai J, Chen Y, Li B, Guo Z, Huang G. Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae. BMC Genomics 2019; 20:782. [PMID: 31660859 PMCID: PMC6819638 DOI: 10.1186/s12864-019-6095-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 09/10/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte. RESULTS In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity. CONCLUSIONS The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.
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Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Xiaobao Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Jimiao Cai
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Yipeng Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Boxun Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Zhikai Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Guixiu Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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Sodré V, Araujo JN, Gonçalves TA, Vilela N, Braz ASK, Franco TT, de Oliveira Neto M, Damasio ARDL, Garcia W, Squina FM. An alkaline active feruloyl-CoA synthetase from soil metagenome as a potential key enzyme for lignin valorization strategies. PLoS One 2019; 14:e0212629. [PMID: 30802241 PMCID: PMC6388921 DOI: 10.1371/journal.pone.0212629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/06/2019] [Indexed: 11/18/2022] Open
Abstract
Ferulic acid (FA), a low-molecular weight aromatic compound derived from lignin, represents a high-value molecule, used for applications in the cosmetic and pharmaceutical industries. FA can be further enzymatically converted in other commercially interesting molecules, such as vanillin and bioplastics. In several organisms, these transformations often start with a common step of FA activation via CoA-thioesterification, catalyzed by feruloyl-CoA synthetases (Fcs). In this context, these enzymes are of biotechnological interest for conversion of lignin-derived FA into high value chemicals. In this study, we describe the first structural characterization of a prokaryotic Fcs, named FCS1, isolated from a lignin-degrading microbial consortium. The FCS1 optimum pH and temperature were 9 and 37°C, respectively, with Km of 0.12 mM and Vmax of 36.82 U/mg. The circular dichroism spectra indicated a notable secondary structure stability at alkaline pH values and high temperatures. This secondary structure stability corroborates the activity data, which remains high until pH 9. The Small Angle X-Ray Scattering analyses resulted on the tertiary/quaternary structure and the low-resolution envelope in solution of FCS1, which was modeled as a homodimer using the hyperthermophilic nucleoside diphosphate-forming acetyl-CoA synthetase from Candidatus Korachaeum cryptofilum. This study contributes to the field of research by establishing the first biophysical and structural characterization for Fcs, and our data may be used for comparison against novel enzymes of this class that to be studied in the future.
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Affiliation(s)
- Victoria Sodré
- Faculty of Chemical Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Thiago Augusto Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Nathália Vilela
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | - Telma Teixeira Franco
- Faculty of Chemical Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mário de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - André Ricardo de Lima Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio Marcio Squina
- Faculty of Chemical Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
- * E-mail:
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Beaton D, Pelletier P, Goulet RR. Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste. Front Microbiol 2019; 10:204. [PMID: 30814985 PMCID: PMC6381020 DOI: 10.3389/fmicb.2019.00204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.
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Affiliation(s)
- Danielle Beaton
- Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, Canada
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
| | | | - Richard R. Goulet
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
- Canadian Nuclear Safety Commission, Ottawa, ON, Canada
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Zhang X, Chen A, Zhang D, Kou S, Lu P. The treatment of flowback water in a sequencing batch reactor with aerobic granular sludge: Performance and microbial community structure. CHEMOSPHERE 2018; 211:1065-1072. [PMID: 30223321 DOI: 10.1016/j.chemosphere.2018.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
The extensive application of hydraulic fracturing technology has significantly promoted the large-scale development of shale gas. However, it is a great challenge for shale gas extraction to effectively manage large-volume flowback water (FW) with high salinity and complex organic substances. Here, we report an aerobic granular sludge (AGS) tolerable to high salinity, and suited to the treatment of FW. The performance of a sequencing batch reactor (SBR) with the AGS for the treatment of the synthetic FW and the microbial community structure at different salinity levels were investigated. The AGS fed with synthetic FW possessed a larger average particle size and a higher settling rate (50 m h-1). When NaCl concentration increased to 50.0 g L-1, the removal efficiency of total organic carbon (TOC) increased to 79 ± 1%, and the removal rate of polyacrylamide (PAM) raised up to 42.7 ± 0.7 g m-3 d-1. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia dominated in the microbial community of AGS. Cellvibrionaceae, Rhodocyclaceae, Enterobacteriaceae, Moraxellaceae, Pseudomonadaceae, and Halomonadaceae belonging to Betaproteobacteria and Gammaproteobacteria played important role in degrading PAM, polycyclic aromatic hydrocarbons (PAH), and some other organics in FW at high salinity. These results suggest that an AGS-based SBR is a promising technology for the treatment of FW.
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Affiliation(s)
- Xiaoting Zhang
- Department of Environmental Science, Chongqing University, Chongqing 400044, China
| | - Aoxiang Chen
- Department of Environmental Science, Chongqing University, Chongqing 400044, China; SHEC City Investment & Development Company Limited, Hubei 430056, China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, Chongqing University, Chongqing 400044, China.
| | - Shuangwu Kou
- Department of Environmental Science, Chongqing University, Chongqing 400044, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, Chongqing University, Chongqing 400044, China
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Sipiczki M, Selim SA. Antagonistic yeasts from a salt-lake region in Egypt: identification of a taxonomically distinct group of phylloplane strains related to Sporisorium. Antonie Van Leeuwenhoek 2018; 112:523-541. [PMID: 30317452 DOI: 10.1007/s10482-018-1184-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/06/2018] [Indexed: 11/28/2022]
Abstract
Non-pathogenic yeasts antagonising microorganisms that cause pre- and postharvest diseases of plants have been found in diverse habitats. Their practical applicability as biocontrol agents (BCAs) depends on the strength of their antagonistic activity and/or spectrum of sensitive target microorganisms. In this study, yeasts were isolated from the phylloplane and fruits of plants growing in the alkaline water lake region Wadi El-Natrun, Egypt, and tested for antifungal and antibacterial activity. All phylloplane yeast isolates belonged to the Basidiomycota and most of them could antagonise at least certain test organisms. One group of isolates showing strong antagonism against almost all fungi and yeasts appears to represent a hitherto undescribed species distantly related to the smut genus Sporisorium. This is the first report of antagonistic activity in Sporisorium. The isolates assigned to Naganishia and Papiliotrema were more effective against bacteria. The broadest range and intensity of antagonism was observed in the fruit-associated strains belonging to the ascomycetous species Wickerhamomyces subpelliculosus. The Wickerhamomyces strains are good broad-spectrum BCA candidates, the Sporisorium strains could be used as efficient antifungal BCAs, whereas the Papiliotrema isolate can be exploited as an antibacterial biocontrol agent.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, 4032, Hungary.
| | - Samy A Selim
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Jouf University, Al-Jouf, Kingdom of Saudi Arabia.,Faculty of Science, Botany Department, Suez Canal University, Ismailia, Egypt
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