Involvement of the metabolically active bacteria in the organic matter degradation during olive mill waste composting

Bacterial community driven nitrogen cycling in coastal sediments of intertidal transition zone

Microorganisms inhabiting in coastal sediments significantly affect the nitrogen cycling in coastal waters and ecosystems. However, the bacterial community that related to the key active nitrogen transformation processes in intertidal transition zone are still not understood. Across a long flat intertidal zone at depths from 0 to 3 m in Daya Bay, China, the bacterial communities in sediments and their driven nitrogen cycling potential were evaluated with environmental factors and 16S rRNA sequencing. The results showed that the intertidal zone is a divide for environmental factors as pH, salinity and C/N ratio, instead of an average shift from freshwater to salt water. At the same time, the environmental factors influenced the abundance of bacterial community related to nitrogen cycling. Across the intertidal zone, the dominant nitrogen transformation processes were different. At the high tide and middle tide sites, the primary nitrogen cycling process was nitrification that worked with Nitrosomonadaceae, Nitrospiraceae, 0319-6A21, and wb1-A12. At the low tide sites, nitrogen fixation was the dominant function conducted by Bradyrhizobiaceae. The reduction of nitrate was carried out with the help of Xanthomonadales but relatively weak in all sampling sites especially for low tide sites. This was mostly because the richness and evenness of bacterial community were the lowest at the low tide sites. Meanwhile, the pH, Cl-, salinity, NH4+, NO3- and C/N ratio were the important factors that shaped the composition of local bacterial community. Further, the nonmetric multidimensional scaling results indicated that there were significant statistical differences in the composition of bacterial community among samples at different layers. The dominant nitrogen cycling processes in coastal sediments at different tide levels were revealed in this study, which offered an extended concept of nitrogen transformation along the groundwater discharge path in the intertidal transition zone. The distributions and compositions of bacterial communities and predicted functions provided a new insight for coastal environment and ecosystem management.

Exploring the humification process of municipal sludge in hyperthermophilic composting through metagenomic and untargeted metabolomic

Hyperthermophilic composting (HC) has been widely recognized for the advantage of high treatment efficiency for organic wastes. However, the humification process is still unclear. In this study, the humification process of HC was investigated, compared to conventional composting (CK). The results showed that the highest composting temperature, organic matter degradation rate, and humification index in HC were 92.62 °C, 23.98%, and 1.59, while those in CK were 70.23 °C, 14.49 %, and 1.04, indicating HC accelerated humification process. Moreover, the results of metagenomic and untargeted metabolomic showed that the genes and metabolisms related to carbohydrate, lipid, amino acid, fatty acid, and nucleotide were more abundant in HC. Consequently, the metabolic pathways regarding organic matter degradation and microbial reproduction were enhanced in the high temperature stage of HC, further accelerating the humification reaction in the low temperature stage. This work contributes to the comprehension of the humification mechanism in HC.

The characteristics and metabolic potentials of the soil bacterial community of two typical military demolition ranges in China

The response mechanism of soil microbiota in military polluted sites can effectively indicate the biotoxicity of ammunition. In this study, two military demolition ranges polluted soils of grenades and bullet were collected. According to high-throughput sequencing, after grenade explosion, the dominant bacteria in Site 1 (S1) are Proteobacteria (97.29 %) and Actinobacteria (1.05 %). The dominant bacterium in Site 2 (S2) is Proteobacteria (32.95 %), followed by Actinobacteria (31.17 %). After the military exercise, the soil bacterial diversity index declined significantly, and the bacterial communities interacted more closely. The indigenous bacteria in S1 were influenced more compared to those in S2. According to the environmental factor analysis, the bacteria composition can easily be influenced by heavy metals and organic pollutants, including Cu, Pb, Cr and Trinitrotoluene (TNT). About 269 metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in bacterial communities, including nutrition metabolism (C, 4.09 %; N, 1.14 %; S, 0.82 %), external pollutant metabolism (2.52 %) and heavy metal detoxication (2.12 %), respectively. The explosion of ammunition changes the basic metabolism of indigenous bacteria, and heavy metal stress inhibits the TNT degradation ability of bacterial communities. The pollution degree and community structure influence the metal detoxication strategy at the contaminated sites together. Heavy metal ions in S1 are mainly discharged through membrane transporters, while heavy metal ions in S2 are mainly degraded through lipid metabolism and biosynthesis of secondary metabolites. The results obtained in this study can provide deep insight into the response mechanism of the soil bacterial community in military demolition ranges with composite pollutions of heavy metals and organic substances. CAPSULE: Heavy metal stress changed the composition, interaction and metabolism of indigenous communities in military demolition ranges, especially the TNT degradation process.

Co-composting of faecal sludge and carbon-rich wastes in the earthworm's synergistic cooperation system: Performance, global warming potential and key microbiome

Composting is an effective alternative for recycling faecal sludge into organic fertilisers. A microflora-earthworm (Eisenia fetida) synergistic cooperation system was constructed to enhance the composting efficiency of faecal sludge. The impact of earthworms and carbon-rich wastes (rice straw (RS) and sawdust (S)) on compost properties, greenhouse gas emissions, and key microbial species of composting were evaluated. The addition of RS or S promoted earthworm growth and reproduction. The earthworm-based system reduced the volatile solid of the final substrate by 13.19-16.24 % and faecal Escherichia coli concentrations by 1.89-3.66 log10 cfu/g dry mass compared with the earthworm-free system. The earthworm-based system increased electrical conductivity by 0.322-1.402 mS/cm and reduced C/N by 56.16-64.73 %. The NH₄⁺:NO₃^- ratio of the final faecal sludge and carbon-rich waste was <0.16. The seed germination index was higher than 80 %. These results indicate that earthworms contribute to faecal sludge maturation. Earthworm addition reduced CO₂ production. The simultaneous addition of earthworms and RS system (FRS2) resulted in the lowest global warming potential (GWP). The microbial diversity increased significantly over time in the RS-only system, whereas it initially increased and later decreased in the FRS2 system. Cluster analysis revealed that earthworms had a more significant impact on the microbial community than the addition of carbon-rich waste. Co-occurrence networks for earthworm-based systems were simple than those for earthworm-free systems, but the major bacterial genera were more complicated. Highly abundant key species (norank_f_Chitinophagaceae and norank_f_Gemmatimonadaceae) are closely related. Microbes may be more cooperative than competitive, facilitating the conversion of carbon and nitrogen in earthworm-based systems. This work has demonstrated that using earthworms is an effective approach for promoting the efficiency of faecal sludge composting and reducing GWP.

Dynamic changes of gut bacterial communities present in larvae of Anoplophora glabripennies collected at different developmental stages

The Asian long-horned beetle, Anoplophora glabripennies (Motschulsky), is a destructive wood-boring pest that is capable of killing healthy trees. Gut bacteria in the larvae of the wood-boring pest is essential for the fitness of hosts. However, little is known about the structure of the intestinal microbiome of A. glabripennies during larval development. Here, we used Illumina MiSeq high-throughput sequencing technology to analyze the larval intestinal bacterial communities of A. glabripennies at the stages of newly hatched larvae, 1st instar larvae and 4th instar larvae. Significant differences were found in larval gut microbial community structure at different larvae developmental stages. Different dominant genus was detected during larval development. Acinetobacter were dominant in the newly hatched larvae, Enterobacter and Raoultella in the 1st instar larvae, and Enterococcus and Gibbsiella in the 4th instar larvae. The microbial richness in the newly hatched larvae was higher than those in the 1st and 4th instar larvae. Many important functions of the intestinal microbiome were predicted, for example, fermentation and chemoheterotrophy functions that may play an important role in insect growth and development was detected in the bacteria at all tested stages. However, some specific functions are found to be associated with different development stages. Our study provides a theoretical basis for investigating the function of the intestinal symbiosis bacteria of A. glabripennies.

Effects of additives on the co-composting of forest residues with cattle manure

Co-composting of forest residues (FR) with cattle manure (CM) results in a low nitrogen (N) conversion efficiency, a low organic matter (OM) degradation rate, and a low quality compost product. This study evaluated the effects of addition of bone charcoal (BC), pumice (PM), or straw biochar (SB) at a ratio of 10 % (w/w) on the co-composting of FR with CM. The highest quality compost was obtained with addition of 10 % PM. Compared with the control (without any additive), PM addition increased the OM degradation rate, the nitrate-N, the available phosphorus, and the available potassium by 25 %, 110 %, 24 %, and 9 %, respectively, and increased the relative abundance of bacteria (Planomicrobium, Flavobacterium, and Pseudomonas) involved in lignocellulose degradation and N transformation. With the addition of PM, the co-composting of FR with CM generated a high quality, useful product in only 39 days.

Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting

Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.

Deciphering the dominant components and functions of bacterial communities for lignocellulose degradation at the composting thermophilic phase

The decomposition and transformation of organic matters during composting process are performed by various microorganisms. However, the bacterial communities and their functions usually vary with composting materials. Here the dominant bacterial genera and their functions were identified at the thermophilic phase during composting of mulberry branches with silkworm excrement (MSE), pig manure (MPM) and cow manure (MCD). The activities of β-glucosidase and endoglucanase were highest for MCD (1.31 and 17.15 µg g^-1 min^-1) and lowest for MPM (0.92 and 14.22 µg g^-1 min^-1). Random Forest model and correlation analysis revealed that Stenotrophomonas, Bacillus, and Sinibacillus were the dominant bacterial genera involved in lignocellulose degradation regardless of composting materials. Carbohydrate metabolism, amino acid metabolism, and DNA replication and repair were primary functions of the bacterial communities for the three types of composting. The quantification of lignocellulose degradation genes further verified the dominant functions of the bacterial communities.

Bacterial dynamics and functions driven by bulking agents to enhance organic degradation in food waste in-situ rapid biological reduction (IRBR)

This study investigated the effects of different bulking agents (i.e., sawdust, wheat straw, rice straw, and corncob) on bacterial structure and functions for organic degradation during food waste in-situ rapid biological reduction (IRBR) inoculated with microbial agent. Results showed that the highest organic degradation (409.5 g/kg total solid) and volatile solids removal efficiency (41.0%) were achieved when wheat straw was used, largely because the degradation of readily degradable substrates and cellulose was promoted by this bulking agent. Compared with other three bulking agents, the utilization of wheat straw was conducive to construct a more suitable environmental condition (moisture content of 18.0-28.2%, pH of 4.91-5.87) for organic degradation during IRBR process, by virtue of its excellent structural and physiochemical properties. Microbial community analysis suggested that the high-moisture environment in rice straw treatment promoted the growth of Staphylococcus and inhibited the activity of the inoculum. By contrast, lowest bacterial richness was observed in corncob treatment due to the faster water loss. Compared with these two bulking agents, sawdust and wheat straw treatment led to a more stable bacterial community structure, and the inoculated Bacillus gradually became the dominant genus (36.6-57.8%) in wheat straw treatment. Predicted metagenomics analysis showed that wheat straw treatment exhibited the highest carbohydrate metabolism activity which improved the pyruvate, amino sugar and nucleotide sugar metabolism, and thereby promoted the organic degradation and humic substrate production. These results indicated that wheat straw was a more desirable bulking agent, and revealed the potential microbial organics degradation mechanism in IRBR process.

Different biodegradation potential and the impacted soil functions of epoxiconazole in two soils

Epoxiconazole is an effective pesticide to control Fusarium head blight (FHB), and the application will increase. To investigate the ecotoxicity of epoxiconazole to soil microbiome, we carried out an indoor experiment in which soils from two main regions of wheat production in China (Nanjing and Anyang) were treated with epoxiconazole (0, 0.0625, 0.625, or 6.25 mg kg^-1) and incubated for 90 days. Under epoxiconazole stress, for bacteria and fungi, the abundance was increased and the diversity and community were impacted. In Anyang soil, the half-life of epoxiconazole was short with more increased species (linear discriminant analysis effect size biomarkers) and more increased xenobiotics biodegradation pathways in epoxiconazole treatments. The increased species mostly due to high abundance in initial state and more positive connections of the species. Co-occurrences revealed that epoxiconazole tightened bacterial connection, and increased positive correlations in Anyang soil. The N transformation was influenced with increased nifH and amoA; and the contents of NH₄⁺-N and NO₃^--N were also increased. The functions of C, S, and manganese metabolisms were also impacted by epoxiconazole. This work expands our understanding about epoxiconazole degradation and help us to properly assess the risk of epoxiconazole in soil.