Correction: Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Martins, Luciane; Antunes, Luciana Principal; Pascon, Renata C.; Oliveira, Júlio Cézar Franco de; Digiampietri, Luciano Antônio; Barbosa, Deibs; Peixoto, Bruno Malveira; Vallim, Marcelo A.; Viana-Niero, Cristina; Ostroski, Eric H.; Telles, Guilherme P.; Dias, Zanoni; Cruz, JoÃ£o Batista da; Juliano, Luiz; Verjovski-Almeida, Sérgio; Silva, da; Setúbal, João Carlos

doi:10.1371/annotation/2cca811e-d45b-4854-a420-d0405309ef43

Cited by 17 publications

(9 citation statements)

References 70 publications

(98 reference statements)

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“…Physicochemical factors, such as temperature, oxygen, moisture, composting materials, and the C/N ratio, are known to affect microbial community changes in cultivation systems and in the development of mushrooms in substrates [134], or vice versa. A complex microbial community can affect composting structure changes, including temperature, pH, aeration, water content, and organic matter [135]. The analysis and study of microbial diversity and metabolism in fermented substrates will provide technical support for effective culture material preparation, and promote industrial mushroom cultivation.…”

Section: Microbial Community Influence On Mushroom Cultivationmentioning

confidence: 99%

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Suwannarach

Kumla

Zhao

et al. 2022

Biology

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Lignocellulosic materials commonly serve as base substrates for mushroom production. Cellulose, hemicellulose, and lignin are the major components of lignocellulose materials. The composition of these components depends upon the plant species. Currently, composted and non-composted lignocellulosic materials are used as substrates in mushroom cultivation depending on the mushroom species. Different substrate compositions can directly affect the quality and quantity of mushroom production yields. Consequently, the microbial dynamics and communities of the composting substrates can significantly affect mushroom production. Therefore, changes in both substrate composition and microbial diversity during the cultivation process can impact the production of high-quality substrates and result in a high degree of biological efficiency. A brief review of the current findings on substrate composition and microbial diversity for mushroom cultivation is provided in this paper. We also summarize the advantages and disadvantages of various methods of mushroom cultivation by analyzing the microbial diversity of the composting substrates during mushroom cultivation. The resulting information will serve as a useful guide for future researchers in their attempts to increase mushroom productivity through the selection of suitable substrate compositions and their relation to the microbial community.

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Section: Microbial Community Influence On Mushroom Cultivationmentioning

confidence: 99%

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Suwannarach

Kumla

Zhao

et al. 2022

Biology

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“…Corynebacterium nuruki was isolated from an alcohol fermentation starter, which was a mixture of grains and various micro-organisms including mold, yeast, and bacteria (Shin). There was a significant dominance of members of the Lactobacillus genus (L. brevis, L. plantarum, L. oris, and L. johnsonii) and Lactobacillus acidipiscis as a minor species [63]. It appeared that Corynebacterium nuruki and Lactobacillus acidipiscis originated from the rice bran used for composting materials in this study.…”

Section: Discussionmentioning

confidence: 61%

The Efficacy of Functional Composts Manufactured Using Spent Coffee Ground, Rice Bran, Biochar, and Functional Microorganisms

2021

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Spent coffee grounds (SCGs), one of the world’s most discarded wastes, may be an excellent resource as an organic fertilizer because of its richness in nutrients. The objective of this study was to develop a quality functional compost using SCGs, rice bran, biochar, SCG extract, and functional microbes (plant growth promoting and plant pathogen-suppression bacteria), and then to test their functional efficacy for a potential commercial application. Essentially, two types of representative composts (Tr_1 and Tr_5 on the laboratory and pilot scale, respectively) were developed and passed all the official commercial quality standards. For pilot-scale composting, populations of Halotalea_uc, Corynebacterium nuruki, and Lactobacillus acidipiscis increased by augmentation of the composting microbes (MA-1) and the functional microbes (Bacillus cereus SB-3, Bacillus toyonensis SB-4, and Streptomyces sasae St-3). The higher total flavonoid content (11% increase compared to control) of pepper leaves in PT-1 and the higher TEAC in PT-1 (36.2%) and PT-2 (32.5%) proved the efficacy of the functional composts bioaugmented with the functional microbes. The seedling growth of radish seeds treated with Streptomyces sasae St-3 as a biocontrol agent significantly increased despite the presence of the pathogen Fusarium oxysporum f. sp. lactucae. The total phenol content and TEAC in pepper plant leaves were significantly higher in Tr_5 than in the control (Tr_4), whereas there were no differences in Tr_4 and Tr_5 infested with the fungal pathogens, indicating that SB-3, SB-4, and St-3 cultures amended within the compost (Tr_5) may facilitate the production of the antioxidants in the absence of the pathogens. However, a significant reduction in the antioxidants (total phenolic content and TEAC) was observed in the pepper plants whose roots were infected with the pathogens, indicating that the pathogens could neutralize functionalities of the functional microbes. It was concluded that the enhancement of functional microbes in the compost would aid in the biological control of pathogens in the soil environment. Further functional compost studies are necessary in terms of mechanisms of plant growth-promotion, mechanisms of pathogen suppression by the actinobacterial biocontrol agents, and interactions between the two mechanisms, as well as quality enhancement of the composts.

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“…The putative ORF (489 amino acids; 55 kDa) from pFos-H4 shared 100% amino acid identity with a sequence derived from a Brazilian compost metagenome (QGUR01000024.1) which, although reported on earlier [22], was only recently added to the NCBI database (June 2018). One of the pFos-H4 end sequences also matched 100% at nucleotide level to the metagenomic contig this gene was located on, suggesting that AFase-H4 originates from a closely related bacterium.…”

Section: Resultsmentioning

confidence: 94%

Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome

et al. 2019

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Background The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. Results Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0–6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed K M range between 0.31 mM and 0.43 mM, K cat range between 131 s − 1 and 219 s − 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside. Conclusion All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study. Electronic supplementary material The online version of this article (10.1186/s12896-019-0510-1) contains supplementary material, which is available to authorized users.

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Correction: Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Cited by 17 publications

References 70 publications

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

The Efficacy of Functional Composts Manufactured Using Spent Coffee Ground, Rice Bran, Biochar, and Functional Microorganisms

Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome

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