Microbial Communities In Compost Research Articles

Control of nitrogen and odor emissions during chicken manure composting with a carbon-based microbial inoculant and a biotrickling filter

Although aerobic composting is usually utilized in livestock manure disposal, the emission of odorous gases from compost not only induces harm to the human body and the environment, but also causes loss of nitrogen, sulfur, and other essential elements, resulting in a decline in product quality. The impact of biotrickling filter (BTF) and insertion of carbon-based microbial agent (CBMA) on compost maturation, odor emissions, and microbial population during the chicken manure composting were assessed in the current experiment. Compared with the CK group, CBMA addition accelerated the increase in pile temperature (EG group reached maximum temperature 10 days earlier than CK group), increased compost maturation (GI showed the highest increase of 41.3% on day 14 in EG group), resulted in 36.59% and 14.60% increase in NO3−-N content and the total nitrogen retention preservation rate after composting. The deodorization effect of biotrickling filter was stable, and the removal rates of NH3, H2S, and TVOCs reached more than 90%, 96%, and 56%, respectively. Furthermore, microbial sequencing showed that CBMA effectively changed the microbial community in compost, protected the ammonia-oxidizing microorganisms, and strengthened the nitrification of the compost. In addition, the nitrifying and denitrifying bacteria were more active in the cooling period than they were in the thermophilic period. Moreover, the abundance of denitrification genes containing nirS, nirK, and nosZ in EG group was lower than that in CK group. Thus, a large amount of nitrogen was retained under the combined drive of BTF and CBMA during composting. This study made significant contributions to our understanding of how to compost livestock manure while reducing releases of odors and raising compost quality.

Role of Microbial Communities in Compost and Plant Growth: Structure and Function

The review explores the microbial communities within composite composts, focusing on their role in decomposition and nutrient cycling, using advanced molecular techniques and traditional microbiological assays, the researchers examine the diverse bacteria, fungi, and archaea in compost matrices, they highlight the richness and complexity of these ecosystems, their adaptability to various environmental conditions, and their substrate compositions. Certain important groups of microorganisms are essential for breaking down organic material, releasing nutrients, and creating humic substances that are vital for soil health and plant development. The research also shows how the makeup of the microbial community and the conditions of composting work together, which has a big impact on how well the compost matures and how good the final product is.

Inhibition of pathogenic microorganisms in solid organic waste via black soldier fly larvae-mediated management

Inadequately managed solid organic waste generation poses a threat to the environment and human health globally. Biotransformation with the black soldier fly larvae (BSFL) is emerging as talent technology for solid waste management. However, there is a lack of understanding of whether BSFL can effectively suppress potential pathogenic microorganisms during management and the underlying mechanisms. In this study, we investigated the temporal variations of microorganisms in two common types of solid waste, i.e., kitchen waste (KW) and pig manure (PM). Natural composting and composting with BSFL under three different pH levels (pH 5, 7, and 9) were established to explore their impact on microbial communities in compost and the gut of BSFL. The results showed that the compost of kitchen waste and pig manure led to an increase in relative abundance of various potentially pathogenic bacteria. Temporal gradient analyses revealed that the most substantial reduction in the relative abundance and diversity of potentially pathogenic microorganisms occurred when the initial pH of both two wastes were adjusted to 7 upon the introduction of BSFL. Through network and pls-pm analysis, it was discovered that the gut microbiota of BSFL occupied an ecological niche in the compost, inhibiting the proliferation of potentially pathogenic microorganisms. This study has revealed the potential of BSFL in reducing public health risks during the solid waste management process, providing robust support for sustainable waste management.

β-Glucosidase-producing microbial community in composting: Response to different carbon metabolic pressure influenced by biochar

Poor management of agricultural waste will cause a lot of environment pollution and the composting process is one of the most effective measures for resource reuse of agricultural waste. β-Glucosidase-producing microbial communities play a vital role in cellulose degradation during composting and regulate cellulase production via differentially expressed glucose/non-glucose tolerant β-glucosidase genes. Biochar is widely used as an amendment in compost to accelerate cellulose degradation during composting. However, Biochar-mediated impacts on β-glucosidase-producing microbial communities in compost are unclear. Here, different carbon metabolism pressures were set in natural and biochar compost to elucidate the regulation mechanism and interaction of the β-glucosidase microbial community. Results showed that the addition of biochar decreased the transcription of β-glucosidase genes and led to a reduction of β-glucosidase activity. Micromonospora and Cellulosimicrobium were the predominant functional communities determining cellulose degradation during biochar compost. Biochar addition strengthened the response of the functional microbial community to carbon metabolism pressure. And adding biochar altered the key β-glucosidase-producing microbial communities, influencing cellulase and the interaction between these communities to respond to the different carbon metabolic pressure of compost. Biochar also shifted the co-occurrence network of β-glucosidase-producing microbial community by changing the keystone species. Furthermore, co-occurrence network analysis revealed that high glucose decreased the complexity and stability of the functional microbial network. Most functional microorganisms from Streptomyces produce non-glucose tolerant β-glucosidase, which were the key bacterial communities affecting β-glucosidase activity in the non-glucose treatment. This study provides new insights into the response of functional microbial communities and the regulation of enzyme production during the transformation of cellulosic biomass.

Manipulating Agaricus bisporus developmental patterns by passaging microbial communities in complex substrates.

There is growing interest in microbiome-based management approaches for plant and animal health and sustainable agricultural practices. To our knowledge, there are no descriptions of Agaricus bisporus mushroom developmental patterns using such an approach. Here, we utilized substrate passaging to select for devomes (developmental microbiomes) in either compost or casing material that resulted in earlier developing (best performing experimental units with a higher number of primordia at day 10 of cultivation) mushrooms compared to unpassaged controls. Passaged casing showed earlier pinning (fruiting body formation), while passaged compost delayed fruiting body formation. Despite changes in pin emergence for passaged substrates and higher mushroom yield in the passaged casing's first harvest, the total mushroom yield in 24 days of crop cycle did not change significantly. The bacterial communities were distinct between compost and casing materials, but in both microenvironments, the alpha diversity tended to increase and stabilize over time in standard and passaged substrates. Community composition within compost and casing microenvironments tended to be more homogenous after colonization of the fungus. Passaging of casing increased the bacterial alpha diversity and shifted community composition. Such changes were not observed in passaged compost. Some bacterial taxa were enriched or depleted by passaging, e.g., Pseudomonas spp. (hypothesized as a stimulus to A. bisporus fructification) were depleted in passaged compost and casing. Overall, this work presents an experimental approach to manipulate compost and casing microbial communities with the potential to be combined with currently employed cultivation strategies toward a more sustainable mushroom cultivation system. IMPORTANCE Agaricus bisporus is an economically important edible mushroom and manipulating its developmental patterns is crucial for maximizing yield and quality. One of the potential strategies for achieving such a goal is passaging microbial communities in compost or casing. The current study demonstrated that passaging substrates develop enriched microbial communities, and after a few passages, certain levels of changes in mushroom developmental patterns (the timing of fruiting bodies formation) were observed as well as shifts in the bacterial communities. Overall, a better understanding of the complex interactions between microorganisms present in the cultivation system may help farmers and researchers to develop more efficient and sustainable cultivation practices that can both benefit the environment and human health.

Fractional grey unequal-interval time-varying Lotka-Volterra model and its application for microbial communities in compost

Aerobic compost is an effective method for the treatment of livestock manure, which is usually accompanied by complex interspecific competition. Describing these competitive relationships through mathematical models can help understand the interaction of microorganisms and analyze the effect of exogenous additive to regulate the composting process. The common model for analyzing competition problem is the Lotka-Volterra model. However, the fixed parameters of the Lotka-Volterra model are not suitable to reflect the dynamic variations of the competitive relationship when the environmental conditions change during composting process. Therefore, this paper establishes a novel fractional grey unequal-interval time-varying Lotka-Volterra model. Firstly, a fractional grey derivate operator is proposed on the basis of the unequal interval of composting data and historical dependence of microbial growth. Secondly, considering the influence of temperature, a time-varying parameter matrix is defined to reflect the variation of competitive relationship at different composting phases, and it is estimated by forgetting factor recursive least squares. Thirdly, the optimal coefficients are optimized by grey prediction evolution algorithm. Finally, the proposed model is employed to analyze the chicken manure composting experiment. The results show that the proposed model has lower error criteria and more accurate trend of fitting curve than the other five existing models. The parameter matrix describes the dynamical variation of microbial competitive relationship in two taxonomic levels and reveals that effect of the exogenous additive is principally reacted in the thermophilic phase and the competitive advantage is shifted from Bacteroidota to Firmicutes after treatment with the exogenous additive.

Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost.

The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional communities between the two composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from the DNA and RNA pools. Principal component analysis and Pearson's correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited a weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. The correlation results suggested that β-glucosidase genes belonging to Micrococcales play an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes and were reflected at both the individual and group levels.

Combined analysis of microbial community and microbial metabolites based on untargeted metabolomics during pig manure composting.

Compost has been widely used in agriculture in recent years, but the nutrients it provides are far from enough for plant growth. Therefore, it is necessary to systematically explore the fermentation process of composting. In this study, the succession of microbial community and metabolite characteristics in compost were analyzed by using microbial sequencing and metabolomics techniques. The results showed that compared with mesophilic phase and cooling phase, the richness and diversity of bacterial community decreased in thermophilic phase. At the genus level, Pseudomonas (8.90%), Lactobacillus (3.99%), Bacteroidetes (3.39%), Flavobacterium (3.25%) and Prevotella (Prevotella_9, 2.33%, Prevotellaceae_NK3B31_group, 2.44%) were the dominant genera in the pig manure composting. The abundance of Pseudomonas and Flavobacterium increased significantly while Lactobacillus and Prevotella were significantly decreased after composting, and the abundance of Bacteroidetes increased first and then decreased. Fatty acyls, sterol lipids, glycerophospholipids, polyketides and prenol lipids were common microbial metabolites in compost. Moreover, the linoleic acid metabolic pathway was significantly enriched in the three stages of composting, and linoleic acid metabolism might be the primary function of the microbial community in composting. The network analysis showed that between the microbial communities or between the microbial community and metabolites were closely related to each other.

Effect of microbial transformation induced by metallic compound additives and temperature variations during composting on suppression of soil-borne pathogens

Agricultural wastes can be modified by composting and reused in soil to suppress soil-borne pathogens, which was proved to be closely related with microbial parameters. However, the microbial community in compost can be directly altered by temperature variations and metallic compound additives during composting process. The present study collected samples in various stages of the 35-day composting process, in which a study control (no additives) and different metallic compound additives, including magnesium oxide (MgO), alum (AlK(SO4)3), calcium oxide (CaO) and ferrous sulfate (FeSO4), were set in the bespoke compost with cow dung and corn stalk. The results showed that the additives prolonged the composting maturity process, whereas no consistent influence on the temperature variation and microbial community was observed. Temperature variations during composting significantly varied the bacteria and fungi diversity and community, especially the bacteria phyla of Firmicutes and Proteobacteria, while the bacteria were shown similar in Day 14 and Day 35 by PCA analysis. Meanwhile the samples from Day 14 and Day 35 showed stable suppressive effects on R. solani. and F. oxysporum, especially in D14 shown as 73.12%–88.16% and 30.95–58.55%, respectively, which were significantly related with the phyla of Firmicutes and Proteobacteria. In conclusion, temperature variations during composting process had a more significant impact than metallic compound additives on the microbial community and diversity, which resulted in significantly influence on the pathogen suppression. Suitable composting duration could produce effective suppressive products on soil-borne pathogens, for which further study was needed.

Microbial Diversity in Compost is Critical in Suppressing Plant Fungal Pathogen Survival and Enhancing Cucumber Seedling Growth

ABSTRACTCompost is commonly used in agriculture to improve soil quality and enhance plant growth, which is considered to be related to microbial communities in compost. However, effects of microbial communities in compost on infecting microorganisms have remained underexplored. In this study, cucumber seedlings were grown in sterilized potting mix amended with sterilized straw composts inoculated with suspensions (4 dilution levels including 100, 10−3, 10−6, and 10−9) of the same compost that was not sterilized. Cucumber seedlings were challenged by a pathogenic F. oxysporum f. sp. radicis-cucumerinum. The microbial communities were evaluated by using a 16 S rRNA multiplex 454 pyrosequencing approach. In general, in the presence of F. oxysporum sp. radicis-cucumerinum, increasing dilution level increased disease severity index and decreased plant productivity. The logarithmic numbers of F. oxysporum sp. radicis-cucumerinum were significantly negatively correlated with the bacterial phylum and OTU (Operational taxonomic unit) richness in compost. The promotion of F. oxysporum sp. radicis-cucumerinum survival in compost with low microbial diversity, might be related to loss of antagonistic activity (as reflected by the copy numbers of the genes rhlB and hcnBC), which was caused by loss of microbial diversity in compost. In summary, microbial diversity in compost is critical in suppressing plant pathogen survival and then enhancing cucumber seedling growth.

The structural and functional contributions of \u03b2-glucosidase-producing microbial communities to cellulose degradation in composting

BackgroundCompost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated.ResultsCompared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content.ConclusionThis research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure–rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.

Nematode and microbial communities in a rapidly changing compost environment: How nematode assemblages reflect composting phases

The microbial community (fungi and bacteria) is the main decomposer of organic matter during composting. Its composition is sometimes used as a proxy to assess compost maturity. Although nematodes are probably its most important grazers, only one previous study has highlighted clear shifts in nematode species composition during composting, and the assumption that nematodes reflect changes in the microbial community in compost has not yet been formally tested. Here, the microbial and nematode communities of a single composting process are analyzed together for the first time. Although both displayed broadly similar patterns, the abundance of fungal-feeding nematodes showed a distinct delay as compared to the increase in fungal PLFA. We argue that the nematode community may be a more promising tool to use in assessing compost maturity because it allows to discriminate between the three composting phases. First, during the thermophilic phase, bacterial-feeding nematodes dominate; during cooling, the bacterial-feeding/predators bloom; and during maturation, the abundance of fungal-feeding nematodes increases. Based solely on the microbial community, it was only possible to discriminate between the thermophilic phase and the rest of the process. Bacteria dominated during the thermophilic phase, while bacterial and fungal PLFA had more-or-less equal shares during cooling and maturation.

Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis

The composting process is carried out under aerobic conditions involving bacteria, archaea, and fungi. Little is known about the diversity of archaeal community in compost, although they may play an important role in methane production and ammonia oxidation. In the present study, archaeal community dynamics during cattle manure composting were analyzed using a clone library of the archaeal 16S rRNA gene. The results indicated that methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA) may be the dominant microbes throughout the composting. The community consisted primarily of Methanocorpusculum-like and Methanosarcina-like sequences until day 2, while the number of Candidatus Nitrososphaera-like sequences increased from day 6 to day 30. Methanosarcina thermophila-like sequences were dominant from day 2, suggesting that M. thermophila-like species can adapt to increasing temperature or nutrient loss. A denaturant gradient gel electrophoresis analysis of the archaeal amoA genes revealed that the dominant amoA gene sequence with 99% homology to that of Candidatus Nitrososphaera gargensis was identical to those obtained from a different composting facility. These data suggested that AOA may play a role in ammonia oxidation in several composting practices. Our results provide fundamental information regarding archaeal community dynamics that will help in understanding the collective microbial community in compost.

Co-composting of manure with fat, oil, and grease: Microbial fingerprinting and phytotoxicity evaluation

Sole carbon source utilization profiles to characterize compost maturity were evaluated in reference to several other physicochemical and biological maturity indices. The results suggested that the addition of fat, oil, and grease (FOG) had a significant effect on the biological processes in the sample piles when compared to the control pile. Additionally, principal components analysis of the patterns and the levels of microbial activity indicate that microbial communities differentiate in response to FOG additions from 1 to 20 L/m3. However, between 10 and 20 L/m3, no recognizable differences were found between the control and the FOG amendment communities. Biolog data indicates a shift in the structure and function of the microbial community in compost with high FOG additions, which may be a useful indicator of high functional diversity and evenness during composting processes. Finally, the germination index (GI) of lettuce increased from 9% in the control to 100% in the FOG amended compost. However, the addition of high amounts of FOG might in turn inhibit seed germination and root growth because of the high pH and electrical conductivity (EC), and the volatilization of NH3. From the present results, 10 L/m3 was found to be the optimum FOG amendment rate for manure compost. These amendment rates are empirical and may be regarded as potential guidelines to agricultural practitioners.

Succession of Actinomycetes During Composting Proccess of Dairy-Farm Waste Investigated by Culture-Dependent and Independent Approaches

Mesophilic, thermophilic, and maturation phases were recognized in composting proccess. Temperature changes influence the microbial communities in compost within composting proccess. Actinomycetes account for a larger part of compost microbial population. The aim of this research was to study succession of actinomycetes community during composting of dairy-farm waste investigated by culture-dependent and independent approaches. In culture-independent method, the succession of actinomycetes community was analyzed by nestedpolymerase chain reaction of ribosomal intergenic spacer (nested-PCR RISA) using spesific primer F243 and primer R23S followed by a second PCR using primers F968 and R23S. In culture-dependent method actinomycetes from compost were isolated on selective media, starch-nitrate medium and humic-acid + vitamins medium. DNA of actinomycetes was extracted and amplified by repetitive sequence-based PCR (rep-PCR) using primer BOXA1R. The banding patterns were used to generate dendrograms by UPGMA clustering with NTSYS program. Microcosm containing sterile rice-straw and water which is inoculated with each actinomycetes isolates was used for examining the ability of each isolate in rice-straw degradation. The experiment results showed that succession of both bacteria and actinomycetes was occured within composting proccess of dairy-farm waste. Analysed by culture-independent method revealed that the highest community of compost’s bacteria was on mesophilic, thermophilic, and maturation phases, respectively. Whereas PCR-nested RISA resulted the highest population of actinomycetes was on thermophilic, maturation, and mesophilic phases, respectively. By culture-dependent method was obtained 29 actinomycetes isolates from mesophilic phase, 23 isolates from thermophilic phase, and 19 isolates from maturation phase. Genetic diversity analysis of the obtained isolates showed the presence of phylogenetic grouping on each phase of composting proccess. This result illustrated the occurance of succession of actinomycetes community in compost. The ability of each isolates in rice-straw degradation was different, and SnT9 isolate was found to be a promising rice-straw degrader. Keywords: succession, actinomycetes, composting, nested-PCR RISA, rep-PCR

Do earthworms affect dynamics of functional response and genetic structure of microbial community in a lab-scale composting system?

Two laboratory-scale systems were set up (i) composting (without earthworms) and (ii) vermicomposting (with earthworms) and were monitored for 60 days after pre-composting. The physico-chemical parameters (pH, C/N, organic matter, NH4+-N and ash content) showed similar evolution in both systems except a higher NH4+-N in the initial vermicomposts. However, principle component analysis (PCA) of enzymatic activities and community level physiological profiles revealed differences in the functional response of microbial communities in compost and vermicompost during maturation. Dehydrogenase activity and bacterial counts indicated a steady decrease in biological activity and population during composting, whereas vermicomposting exhibited higher activity on day 30 and a reduction in bacterial counts on day 10. PCA of denatured gradient gel electrophoresis (DGGE) profiles showed divergent dynamics of bacterial communities in two processes. These results indicated differences in the functional response and genetic structure of microbial community in composts and vermicomposts despite similar changes in their physico-chemical parameters.

Design and application of an oligonucleotide microarray for the investigation of compost microbial communities

A microarray consisting of oligonucleotide probes targeting variable regions of the 16S rRNA gene was designed and tested for the investigation of microbial communities in compost. Probes were designed for microorganisms that have been previously reported in the composting process and for plant, animal and human pathogens. The oligonucleotide probes were between 17 and 25 bp in length and included mostly species-specific sequences. Validation of probe specificity and optimization of hybridization conditions were conducted using fluorescently labeled 16S rRNA gene PCR products of pure culture strains. A labeling method employing a Cy3 or Cy5-labeled forward primer together with a phosphate-conjugated reverse primer for the production of single stranded DNA after a digestion step was optimised and used to label target DNA. A combination of two different DNA extraction methods using both physical and chemical lysis was found to give the best DNA yields. Increased hybridization signal intensities were obtained for probes modified with a 12mer T-spacer. The microarray was found to have a detection limit of 10 3 cells, although in compost spiking experiments, the detection limit was reduced to 10 5 cells. The application of the microarray to compost samples indicated the presence of Streptococcus, Acinetobacter lwoffii, and Clostridium tetani in various compost samples. The presence of A. lwoffii in those compost samples was confirmed by PCR using primers specific for the organism. The aim of this study was to develop a molecular tool that would allow screening for the presence or absence of different microorganisms within compost samples.