Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India

Mehta, Chandra Mohan; Yu, Dan; Sinkkonen, Aki; Kurola, Jukka; Gupta, Varun; Jääskeläinen, Heidi; Palni, Uma T.; Sharma, Anil Kumar; Romantschuk, Martin

doi:10.1080/1065657x.2015.1087894

Cited by 11 publications

(10 citation statements)

References 47 publications

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“…Interestingly, the strong and significant effect of built environment on doormat Gammaproteobacterial community and the slight but significant effect on doormat Firmicutes community disappeared after removing the animal owners from the data. Firmicutes are one of the two dominating phyla in the gut (Ley et al, 2006 ; Zhu et al, 2010 ) and rare or even absent in surface soils, except in composts containing animal dung (Yu et al, 2015 ; Mehta et al, 2016 ), possibly explaining this outcome. Notably, we did extensive literature review to search for the origin of most common 30 Firmicutes OTUs that represented 50% of total Firmicutes OTUs (data not shown).…”

Section: Discussionmentioning

confidence: 99%

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors

et al. 2018

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Expanding urbanization is a major factor behind rapidly declining biodiversity. It has been proposed that in urbanized societies, the rarity of contact with diverse environmental microbiota negatively impacts immune function and ultimately increases the risk for allergies and other immune-mediated disorders. Surprisingly, the basic assumption that urbanization reduces exposure to environmental microbiota and its transfer indoors has rarely been examined. We investigated if the land use type around Finnish homes affects the diversity, richness, and abundance of bacterial communities indoors. Debris deposited on standardized doormats was collected in 30 rural and 26 urban households in and near the city of Lahti, Finland, in August 2015. Debris was weighed, bacterial community composition determined by high throughput sequencing of bacterial 16S ribosomal RNA (rRNA) gene on the Illumina MiSeq platform, and the percentage of four different land use types (i.e., built area, forest, transitional, and open area) within 200 m and 2000 m radiuses from each household was characterized. The quantity of doormat debris was inversely correlated with coverage of built area. The diversity of total bacterial, Proteobacterial, Actinobacterial, Bacteroidetes, and Firmicutes communities decreased as the percentage of built area increased. Their richness followed the same pattern except for Firmicutes for which no association was observed. The relative abundance of Proteobacteria and particularly Gammaproteobacteria increased, whereas that of Actinobacteria decreased with increasing built area. Neither Phylum Firmicutes nor Bacteroidetes varied with coverage of built area. Additionally, the relative abundance of potentially pathogenic bacterial families and genera increased as the percentage of built area increased. Interestingly, having domestic animals (including pets) only altered the association between the richness of Gammaproteobacteria and diversity of Firmicutes with the built area coverage suggesting that animal ownership minimally affects transfer of environmental microbiota indoors from the living environment. These results support the hypothesis that people living in densely built areas are less exposed to diverse environmental microbiota than people living in more sparsely built areas.

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Section: Discussionmentioning

confidence: 99%

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors

et al. 2018

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“…Importantly, recent findings indicate that Proteobacterial community of individual’s skin depends on land use in their living environment and that the environment tunes response to allergens [ 27 – 31 ]. Soil is the major reservoir of Actinobacteria, Bacteroidetes, and Proteobacteria [ 32 , 33 ], and thus the living environment likely tunes individual’s responses to allergens, sugar metabolism, and health disorders. For these reasons, it is possible that adverse health effects connected to living in contaminated environment may partly be attributable to fundamental changes in the environmental microbiome people are exposed to, in addition to the direct physiological responses caused by the toxins.…”

Section: Introductionmentioning

confidence: 99%

The abundance of health-associated bacteria is altered in PAH polluted soils—Implications for health in urban areas?

et al. 2017

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Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic “adverse toxin effect” paradigm and our novel “altered environmental microbiome” hypothesis.

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“…The composts from various sources are well known for their role in suppression of plant diseases and are commonly used as a natural biological control since long time (Grebus et al 1994;Hoitink et al 1997;Vestberg et al 2009;Hadar 2011;Shivlata and Satyanarayana 2017). The disease suppression of compost is considered as a result of two components: one when compost acts as a source for various biochemical compounds such as hormones, antibiotics and other secreted chemicals of microorganism, and secondly the beneficial microbes of compost (Özer and Köycü 2006;Fuchs 2010;Mehta et al 2016;Scotti et al 2016). However, all the composts are not equally effective towards disease suppression since they carry a huge difference in biochemical and microbial activities (Mupambwa et al 2016;Tossavainen et al 2017).…”

Section: Introductionmentioning

confidence: 99%

“…There are many studies where the researchers have explored the microbial diversity of different compost and soil by using molecular tools (Nannipieri et al 2003;Mehta et al 2014;Pudasaini et al 2017). Differential gradient gel electrophoresis (DGGE) is one of the most commonly used techniques in diversity studies (Yu et al 2015;Mehta et al 2016). Previous studies have implied that molecular biology approaches could be effectively used for improved understanding of disease suppression by compost (Blaya et al 2016;Ros et al 2017).…”

Section: Introductionmentioning

confidence: 99%

“…In previous studies, our laboratory has identified few types of compost that suppressed the occurrence of Fusarium wilt in tomato. Through DGGE profiling of compost, specific bacterial community was observed in highly disease-suppressive compost (Mehta et al 2016). Based on available information, this study was carried out to develop closely linked PCR-based molecular markers that can be used to detect specific microbial community in composts.…”

Section: Introductionmentioning

confidence: 99%

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Development of PCR-based molecular marker for screening of disease-suppressive composts against Fusarium wilt of tomato (Solanum lycopersicum L.)

et al. 2018

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The present study was carried out to develop a PCR-based molecular marker suitable for screening of disease-suppressive composts against Fusarium wilt of tomato. An effective uncultured bacterial community was screened from our previous study on investigation of microbial communities in composts for their potential for biocontrol of Fusarium wilt. Based on available sequence information (Accession no. HQ388491) of selective community, PCR-based molecular markers were designed and tested for their specificity in different compost sample. To confirm specificity of designed marker, real-time reverse transcription-PCR (qRT-PCR) analysis was performed. Selective marker efficacy was further tested for different set of composts and results were cross-verified by conducting bioassay of same composts against Fusarium wilt in tomato crop. Results showed that out of two designed set of primers (i.e., PAC1F/PAC1R and PAC4F/PAC4R), primer set PAC4F/PAC4R resulted in successful amplification of 199 bp in highly disease-suppressive compost (i.e., CPP); however, no/below detection level amplification was observed in non-suppressive compost (JC). qRT-PCR analysis confirmed the specificity of selective marker by representing single peak in melting curve. A clear difference was observed in relative population of selective community in different set of composts. It was observed maximum in the most effective compost, i.e., CPP followed by other disease-suppressive composts. Cross-examination of results with bioassay confirmed that composts with presence of selective bacterial community having no/very less disease incidence of Fusarium. It is clearly evident from the study that such kind of molecular markers can be developed and used in future research focusing on compost-based disease suppression.

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Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India

Cited by 11 publications

References 47 publications

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors

The abundance of health-associated bacteria is altered in PAH polluted soils—Implications for health in urban areas?

Development of PCR-based molecular marker for screening of disease-suppressive composts against Fusarium wilt of tomato (Solanum lycopersicum L.)

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