Succession of a microbial community during stable operation of a semi-continuous garbage-decomposing system

Haruta, Shin; Kondo, Michitada; Nakamura, Kohei; Chanchitpricha, Chaunjit; Aiba, Hiroshi; Ishii, Masaharu; Igarashi, Yasuo

doi:10.1016/s1389-1723(04)70237-6

Cited by 15 publications

(6 citation statements)

References 23 publications

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“…Succession in microbial communities has been well documented in microbial mat systems (Stal et al ., 1985; Stolz, 1990; Grootjans et al ., 1997) and is largely influenced by the changes in the environment (Mackie et al ., 1999; Haruta et al ., 2004; Jones and Lennon, 2010; Sato et al ., 2010). Based on the diversity analyses, we propose that the four thrombolitic mat types represent successive stages of thrombolite development in Highborne Cay, Bahamas (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The transitions between mat types may also reflect a shift in the pH, which may result in the differences in the patterns of biologically induced biomineralization. Shifts in pH have been shown to trigger succession events in complex microbial communities (Haruta et al ., 2004) and in the button mats there are numerous ecotypes associated with metabolisms that influence carbonate alkalinity, such as oxygenic, anoxygenic photosynthesis and sulfate reduction (Dupraz et al ., 2009). Together these metabolisms can initiate and promote carbonate precipitation (Dupraz et al ., 2009); however, more work is necessary to monitor the specific changes in pH between the four mat types to assess the impact of pH on each of the thrombolitic mat types.…”

Section: Discussionmentioning

confidence: 99%

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Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Mobberley

Ortega

Foster

2011

Environmental Microbiology

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Thrombolites are unlaminated carbonate structures that form as a result of the metabolic interactions of complex microbial mat communities. Thrombolites have a long geological history; however, little is known regarding the microbes associated with modern structures. In this study, we use a barcoded 16S rRNA gene-pyrosequencing approach coupled with morphological analysis to assess the bacterial, cyanobacterial and archaeal diversity associated with actively forming thrombolites found in Highborne Cay, Bahamas. Analyses revealed four distinct microbial mat communities referred to as black, beige, pink and button mats on the surfaces of the thrombolites. At a coarse phylogenetic resolution, the domain bacterial sequence libraries from the four mats were similar, with Proteobacteria and Cyanobacteria being the most abundant. At the finer resolution of the rRNA gene sequences, significant differences in community structure were observed, with dramatically different cyanobacterial communities. Of the four mat types, the button mats contained the highest diversity of Cyanobacteria, and were dominated by two sequence clusters with high similarity to the genus Dichothrix, an organism associated with the deposition of carbonate. Archaeal diversity was low, but varied in all mat types, and the archaeal community was predominately composed of members of the Thaumarchaeota and Euryarchaeota. The morphological and genetic data support the hypothesis that the four mat types are distinctive thrombolitic mat communities.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Mobberley

Ortega

Foster

2011

Environmental Microbiology

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“…For example, actinomycetes, notably Streptomyces , are known to produce a variety of antibiotics as secondary metabolites. While there have been a few detailed analyses of bacterial community structure throughout the composting process, the majority of studies to date have commonly used either culture-based analysis [79,80,82] or low-resolution molecular techniques (e.g., sequencing clones [15,16] or DGGE analysis [3,18–20]). Only two recent studies have used higher-resolution sequencing methods to evaluate sewage sludge compost [25] or zoo compost [26], and Rawat and Johri [78] have reviewed the literature available before 2013.…”

Section: Discussionmentioning

confidence: 99%

Bacterial community structure transformed after thermophilically composting human waste in Haiti

et al. 2017

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Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

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“…Continual change in the environmental conditions in composts (temperature, pH, aeration, moisture, and availability of substrates) results in different stages of exponential growth and stationary phases for different organisms. Knowledge on the diversity and dynamics of the microbial communities of compost is increasing rapidly through the use of molecular biology tools such as community fingerprinting by amplified rDNA restriction analysis, denaturing gradient gel electrophoresis (DGGE), and DNA hybridization techniques [1,22,40,47].…”

Section: Introductionmentioning

confidence: 99%

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

et al. 2008

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A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.

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Succession of a microbial community during stable operation of a semi-continuous garbage-decomposing system

Cited by 15 publications

References 23 publications

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Bacterial community structure transformed after thermophilically composting human waste in Haiti

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

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