Targeted 16S rRNA high-throughput sequencing to characterize microbial communities during composting of livestock mortalities

Abstract

Aim: A comprehensive understanding of the microbial community is necessary to ensure a significant reduction in pathogens during the composting process. Methods and Results: Two biosecure, static composting systems containing cattle mortalities were constructed at subzero temperatures. Temperature at each sampling site was measured continuously and samples were grouped as either ≤50 or ≥55°C, based on temperature exposure required for effective pathogen inactivation during composting. High-throughput 454 sequencing was used to characterize the bacterial communities within each sample. Clustering of bacterial communities was observed according to temperature. However, neither richness nor diversity differed between temperature groups. Firmicutes was the most abundant phylum within both temperature groups but was more pronounced (63Á6%) in samples ≥55°C (P < 0Á05). Similarly, members of Clostridia, Clostridium sensu stricto (3Á64%), Clostridium XI (0Á59%), UF (Clostridiaceae 1) (5Á29%) and UF (Clostridiales Incertae Sedis XI) (6Á20%), were prominent at ≥55°C (P < 0Á05), likely a reflection of spore survival and/or anaerobic microenvironments within passively aerated compost piles. Members of Thermobifida (3Á54%), UO (Actinomycetales) (12Á29%) and UO (Bacillales) (19Á49%) were also prominent at ≥55°C (P < 0Á05). Conclusion: Substantial spatial diversity exists within bacterial communities in field-scale compost piles. Localized temperature at the site of sampling may be one of the factors contributing to this phenomenon. Significance and Impact of the Study: This is the first study to describe the microbial community profile with the use of targeted 16S rRNA highthroughput sequencing in passively aerated composted livestock mortalities.

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

“…Except for D99, members from the orders Bacillales, Clostridiales, Actinomycetales, and Thermoanaerobacterales abound throughout the composting process, and most CDSs related to plant biomass degradation were classified as belonging to members of these orders. Actinomycetales are commonly found in compost, particularly in the thermophilic and mature stages11162554, and also in thermophilic microbial consortia enriched from compost3055. Indeed, in our data the relative abundance of CDSs assigned to this order involved with lignocellulosic biomass degradation is largest at D30 and D78 (34.4% and 49%, respectively).…”

“…We also feature Thermopolyspora , Thermobispora, and Thermomonospora among the abundant genera within Actinomycetales. These genera comprise bacterial species that can survive the thermophilic stages of composting and are hypothesized to play an important role in biomass degradation during the composting process41213162527282930.…”

“…Despite intensive studies to investigate thermophilic composting ecosystems, using culture-dependent1624 and culture-independent approaches41011131525, information regarding functional aspects of associated microbiota is still limited. In this regard, metagenomics and metatranscriptomics are valuable approaches to expand the repertoire of known biodegrading microorganisms and their active functional metabolic potential during thermophilic composting.…”

Microbial diversity and nitrogen‐metabolizing gene abundance in backyard food waste composting systems

“…In contrast, a study of livestock mortality compost found a predominance of Proteobacteria when temperatures were <50°C (Tkachuk et al . ), suggesting Proteobacteria are very adaptable to the type of pile and the temperature, although they prefer the later mesophilic phase of decomposition.…”

Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying

“…In addition, in the past, the composting microbial community was usually studied using traditional methods such as terminal restriction fragment length polymorphism (T-RFLP), PCR denaturing gradient gel electrophoresis (DGGE), clone library, or culturing methods. As a new method for microbial community structure studies, high-throughput sequencing has increased the capacity and rate of the discovery of unknown microorganisms and given a more comprehensive picture of microbial biodiversity (Petrosino et al 2009) It has been recently used in a few studies on the composting microbial community (Tkachuk et al 2014), but those studies have focused on the start and the end of composting. Information on the evolution of the microbial community throughout the composting process is still deficient.…”