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Chen P, Wan W. Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting. BIORESOURCE TECHNOLOGY 2023; 368:128335. [PMID: 36403913 DOI: 10.1016/j.biortech.2022.128335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China.
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Ai W, Guo T, Lay KD, Ou K, Cai K, Ding Y, Liu J, Cao Y. Isolation of soybean-specific plant growth-promoting rhizobacteria using soybean agglutin and evaluation of their effects to improve soybean growth, yield, and soil nutritional status. Microbiol Res 2022; 261:127076. [PMID: 35636091 DOI: 10.1016/j.micres.2022.127076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022]
Abstract
The basic requirements of plant growth-promoting rhizobacteria (PGPR) for field applications are that they have an affinity for the host plant and that they can colonize the rhizosphere. Here, a new technique was established using soybean agglutin (SBA) as a tool to isolate soybean-specific PGPR. Thirty-three PGPR strains with an affinity for soybean were obtained via the screening method with SBA. All 33 isolates were able to produce indole acetic acid and solubilize inorganic phosphate and potassium. Most isolates (93.94%) were able to solubilize organic phosphate and almost half (45.45%) were able to produce siderophores. More than 40% of the isolates exhibited all five plant growth-promoting traits. The isolate Enterobacter sp. strain DN9 was selected for further analyses of its rhizosphere colonization and soybean growth-promoting effects because of its excellent activity in phosphate and potassium solubilization. The luciferase luxAB gene was electrotransformed into DN9, and the labelled DN9 (DN9-L) was able to survive in the soybean rhizosphere and colonize new spaces as the soybean roots elongated. This strain positively affected root system development and soybean seedling growth. In pot and field experiments, the isolates DN9, DW1, and DW13 significantly increased the nutrient contents in rhizosphere soil and soybean leaves. On average, the seed number per plant and the seed weight per plant were increased by 20% and 24% respectively, in plants inoculated with these PGPR strains in the pot experiment. In a field experiment, compared with uninoculated plants, those inoculated with DW1 showed 46.78% higher pod number per plant and 5.23% higher seed oil content; those inoculated with DW13 showed 79.82% higher seed number per plant and 65.10% higher seed weight per plant; and those inoculated with DN9 showed 9.13% higher 100-seed weight. These results show that SBA can be used as a tool to isolate efficient PGPR to enhance soybean production.
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Affiliation(s)
- Wenfeng Ai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Tingting Guo
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Khien Duc Lay
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Kangmiao Ou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Ke Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yue Ding
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Jia Liu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yuanyuan Cao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China.
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Challacombe JF, Hesse CN, Bramer LM, McCue LA, Lipton M, Purvine S, Nicora C, Gallegos-Graves LV, Porras-Alfaro A, Kuske CR. Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics 2019; 20:976. [PMID: 31830917 PMCID: PMC6909477 DOI: 10.1186/s12864-019-6358-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. RESULTS Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. CONCLUSIONS This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.
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Affiliation(s)
- Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Present address: Colorado State University, College of Agricultural Sciences, 301 University Ave, Fort Collins, CO, 80523, USA.
| | - Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Horticultural Crops Research, USDA ARS, Corvallis, OR, USA
| | - Lisa M Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mary Lipton
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel Purvine
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie Nicora
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | | | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Meng X, Liu B, Xi C, Luo X, Yuan X, Wang X, Zhu W, Wang H, Cui Z. Effect of pig manure on the chemical composition and microbial diversity during co-composting with spent mushroom substrate and rice husks. BIORESOURCE TECHNOLOGY 2018; 251:22-30. [PMID: 29257993 DOI: 10.1016/j.biortech.2017.09.077] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 06/07/2023]
Abstract
In this study, the impact of pig manure on the maturity of compost consisting of spent mushroom substrate and rice husks was accessed. The results showed that the addition of pig manure (SMS-PM) reached 50°C 5days earlier and lasted 15days longer than without pig manure (SMS). Furthermore, the addition of pig manure improved nutrition and germination index. High-throughput 16S rRNA pyrosequencing was used to evaluate the bacterial and fungal composition during the composting process of SMS-PM compared to SMS alone. The SMS treatment showed a relatively higher abundance of carbon-degrading microbes (Bacillaceae and Thermomyces) and plant pathogenic fungi (Sordariomycetes_unclassified) at the end of the compost. In contrast, the SMS-PM showed an increased bacterial diversity with anti-pathogen (Pseudomonas). The results indicated that the addition of pig manure improved the decomposition of refractory carbon from the spent mushroom substrate and promoted the maturity and nutritional content of the compost product.
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Affiliation(s)
- Xingyao Meng
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Bin Liu
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China; UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Chen Xi
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Xiaosha Luo
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Xufeng Yuan
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Xiaofen Wang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Wanbin Zhu
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Hongliang Wang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China
| | - Zongjun Cui
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agriculture University, Beijing 100193, China.
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Molecular advancements in the development of thermostable phytases. Appl Microbiol Biotechnol 2017; 101:2677-2689. [PMID: 28233043 DOI: 10.1007/s00253-017-8195-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022]
Abstract
Since the discovery of phytic acid in 1903 and phytase in 1907, extensive research has been carried out in the field of phytases, the phytic acid degradatory enzymes. Apart from forming backbone enzyme in the multimillion dollar-based feed industry, phytases extend a multifaceted role in animal nutrition, industries, human physiology, and agriculture. The utilization of phytases in industries is not effectively achieved most often due to the loss of its activity at high temperatures. The growing demand of thermostable phytases with high residual activity could be addressed by the combinatorial use of efficient phytase sources, protein engineering techniques, heterologous expression hosts, or thermoprotective coatings. The progress in phytase research can contribute to its economized production with a simultaneous reduction of various environmental problems such as eutrophication, greenhouse gas emission, and global warming. In the current review, we address the recent advances in the field of various natural as well as recombinant thermotolerant phytases, their significance, and the factors contributing to their thermotolerance.
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Qin H, Sun Q, Pan X, Qiao Z, Yang H. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel. Front Microbiol 2016; 7:1311. [PMID: 27610102 PMCID: PMC4997791 DOI: 10.3389/fmicb.2016.01311] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022] Open
Abstract
Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.
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Affiliation(s)
- Huibin Qin
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural SciencesTaiyuan, China
| | - Qinghui Sun
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
| | - Xuewei Pan
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
| | - Zhijun Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural SciencesTaiyuan, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
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Blomqvist J, Leong SLL, Sandgren M, Lestander T, Passoth V. Temperature-dependent changes in the microbial storage flora of birch and spruce sawdust. Biotechnol Appl Biochem 2014; 61:58-64. [PMID: 24527731 DOI: 10.1002/bab.1153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/03/2013] [Indexed: 11/09/2022]
Abstract
Sawdust can be used to make pellets (biofuel) and particle boards and as a potential lignocellulose feedstock in bioethanol production. Microbial activity can affect sawdust quality; hence, we monitored the microbial population in birch- and spruce sawdust after 3 months' storage at various temperatures. Species composition was similar on both materials but was strongly influenced by temperature. Bacteria were present on all materials at all conditions: on birch, 2.8 × 10(8) , 1.1 × 10(8) , and 8.8 × 10(6) , and on spruce, 4.1 × 10(8) , 5.6 × 10(7) , and 1.5 × 10(8) CFU/g DM, at 2, 20, and 37 °C, respectively. Dominant bacteria at 2, 20, and 37 °C were Pseudomonas spp. (some Enterobacteriaceae spp. present), Luteibacter rhizovicinus, and Fulvimonas sp., respectively. Pseudomonas spp. were absent at ≥20 °C. Among microfungi, yeasts dominated at 2 °C but were absent at 37 °C, whereas molds dominated at 20 and 37 °C. Common yeasts included Cystofilobasidium capitatum, Cystofilobasidium infirmominiatum, Candida saitoana, Candida oregonensis, and Candida railenensis. Ophiostoma quercus was a common mold at 2 and 20 °C, whereas the human pathogens Aspergillus fumigatus and Paecilomyces variotii dominated at 37 °C. Attempts to influence the microflora by addition of the biocontrol yeasts, Wickerhamomyces anomalus and Scheffersomyces stipitis, were unsuccessful, as their growth in sawdust was poor to absent.
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Affiliation(s)
- Johanna Blomqvist
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Department of Microbiology, Uppsala, Sweden
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Abstract
A focused platform for phytase bio-processing and application oriented research will help in developing an integrated technological solution to phytase production.
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Affiliation(s)
- K. Bhavsar
- NCIM Resource Center
- National Chemical Laboratory
- Pune 411008, India
| | - J. M. Khire
- NCIM Resource Center
- National Chemical Laboratory
- Pune 411008, India
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Affiliation(s)
- Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, Tsukuba, Japan.
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