Cellulose-degrading bacteria improve conversion efficiency in the co-digestion of dairy and chicken manure by black soldier fly larvae

Black soldier fly larvae (BSFL) have potential utility in converting livestock manure into larval biomass as a protein source for livestock feed. However, BSFL have limited ability to convert dairy manure (DM) rich in lignocellulose. Our previous research demonstrated that feeding BSFL with mixtures of 40% dairy manure and 60% chicken manure (DM40) provides a novel strategy for significantly improving their efficiency in converting DM. However, the mechanisms underlying the efficient conversion of DM40 by BSFL are unclear. In this study, we conducted a holistic study on the taxonomic stucture and potential functions of microbiota in the larval gut and manure during the DM and DM40 conversion by BSFL, as well as the effects of BSFL on cellulosic biodegradation and biomass production. Results showed that BSFL can consume cellulose and other nutrients more effectively and harvest more biomass in a shorter conversion cycle in the DM40 system. The larval gut in the DM40 system yielded a higher microbiota complexity. Bacillus and Amphibacillus in the BSFL gut were strongly correlated with the larval cellulose degradation capacity. Furthermore, in vitro screening results for culturable cellulolytic microbes from the larval guts showed that the DM40 system isolated more cellulolytic microbes. A key bacterial strain (DM40L-LB110; Bacillus subtilis) with high cellulase activity from the larval gut of DM40 was validated for potential industrial applications. Therefore, mixing an appropriate proportion of chicken manure into DM increased the abundance of intestinal bacteria (Bacillus and Amphibacillus) producing cellulase and improved the digestion ability (particularly cellulose degradation) of BSFL to cellulose-rich manure through changes in microbial communities composition in intestine. This study reveals the microecological mechanisms underlying the high-efficiency conversion of cellulose-rich manure by BSFL and provide potential applications for the large-scale cellulose-rich wastes conversion by intestinal microbes combined with BSFL.

Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems

Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.

Di-n-butyl phthalate stress hampers compost multifunctionality by reducing microbial biomass, diversity and network complexity

Phthalates are common pollutants in agriculture. Here, the influence of di-n-butyl phthalate (DBP) on multifunctionality of composting was assessed. Results indicated that DBP stress (100 mg/kg) hampered multifunctionality from the thermophilic phase onwards and resulted in a 6.5 % reduction of all assessed functions. DBP stress also significantly reduced microbial biomass (P < 0.05), altered microbial composition (P < 0.05), and decreased network complexity (P < 0.01). Multifunctionality was found to be strongly correlated (P < 0.001) with microbial biomass, diversity, and network complexity. In addition, keystone taxa responsive to DBP were identified as Streptomyces, Thermoactinomyces, Mycothermus, and Lutispora. These taxa were significantly (P < 0.001) affected by DBP stress, and a correlation between them and multifunctionality was shown. This study contributes to a better understanding of the negative implications of phthalates during composting processes, which is of great significance to the development of new treatment strategies for agricultural waste.

Biochar reduces bioavailability of phosphorus during swine manure composting: Roles of phoD-harboring bacterial community

The bioavailability of phosphorus is a vital index for evaluating the quality of compost products. This study examined the effects of adding wheat straw biochar (WSB) and bamboo charcoal (BC) on the transformation of various phosphorus fractions during composting, as well as analyzing the roles of the phoD-harboring bacterial community in the transformation of phosphorus fractions. Adding WSB and BC reduced the available phosphorus content in the compost products by 35.2 % and 38.5 %, respectively. Redundancy analysis showed that the alkaline phosphatase content and pH were the most important factors that affected the transformation of phosphorus fractions. The addition of biochar resulted in changes in the composition and structures of the phoD-harboring bacteria communities during composting. In addition, the key bacterial genera that secreted alkaline phosphatase and decomposed different forms of phosphorus under WSB and BC were different compared with those under control. Network and correlation analysis demonstrated that the activities of phoD-harboring bacteria could have been enhanced by biochar to accelerate the consumption of available phosphorus, and the activities of key phosphorus-solubilizing bacteria (Lysobacter, Methylobacterium, and Saccharothrix) might be inhibited when the pH increased, thereby increasing the insoluble phosphorus content.

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.

Response of antibiotic resistance to the co-exposure of sulfamethoxazole and copper during swine manure composting

Heavy metals driven co-selection of antibiotic resistance in soil and water bodies has been widely concerned, but the response of antibiotic resistance to co-existence of antibiotics and heavy metals in composting system is still unknown. Commonly used sulfamethoxazole and copper were individually and jointly added into four reactors to explore their effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), heavy metal resistance genes (MRGs) and bacterial community structure. The abundance of total ARGs and MGEs were notably decreased by 68.64%-84.95% and 91.27-97.38%, respectively, after the composting. Individual addition of sulfamethoxazole, individual addition of copper, simultaneously addition of sulfamethoxazole and copper increased the abundance of ARGs and MGEs throughout the composting period. Co-exposure of sulfamethoxazole and copper elevated the total abundance of ARGs by 1.17-1.51 times by the end of the composting compared to individual addition of sulfamethoxazole or copper. Network analysis indicated that the shifts in potential host bacteria determined the ARGs variation. Additionally, MGEs and MRGs had significant effects on ARGs, revealing that horizontal gene transfer and heavy metals induced co-resistance could promote ARGs dissemination.

Dynamics of bacterial and archaeal communities along the composting of tannery sludge

The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.

Effects of Exogenous Microbial Agents on Soil Nutrient and Microbial Community Composition in Greenhouse-Derived Vegetable Straw Composts

Vegetable waste causes resource waste and environmental pollution, giving rise to the spread of harmful organisms and causing disease in normal vegetable cultivation. Random distribution of vegetable waste can increase the risk of non-point agricultural pollution and explore the feasibility of its resource utilization. This study was designed to evaluate the effects of different doses of exogenous microbial agents on soil microbial communities after in situ composting of cucumber straw on plots with biodegradable mulch films. The cucumber straw and chicken manure were used as the base materials, and the next generation sequencing was used to analyze changes in the microbiome following composting. The results demonstrate that the addition of exogenous microbial agents had prolonged the high-temperature duration, reduced the total organic carbon (TOC) content, and accelerated the decline in the C/N ratio, ensuring compost maturity and effectively shortening the composting time. The predominant bacterial phyla of the four treatment groups were Proteobacteria and Firmicutes; while among fungal phyla, these treatments decreased the relative abundance of Ascomycota. The treatment of 300 t/ha microbial agents significantly increased the richness and diversity of both the bacterial and fungal communities. Redundancy analysis suggested that soil total nitrogen (TN) content had a significant effect on the bacterial community, while TN content, pH, and temperature influenced the fungal community in these samples. Collectively, the treatment of 300 t/ha exogenous microbial agents improved the quality of composting and promoted microbiome diversity.

Linking microbial community structure with molecular composition of dissolved organic matter during an industrial-scale composting

This study explored the interactions between dissolved organic matter (DOM) composition and microbial community structure during an industrial-scale composting by Fourier transform ion cyclotron resonance mass spectrometry and 16S rRNA sequencing analysis. The results revealed that DOM from matured compost contained primarily lignins/carboxylic-rich alicyclic molecules (73.6%), the higher double bond equivalent (5.97) and aromaticity index (0.18), indicating that the molecular composition of DOM had changed substantially. Drastic changes in microbial community structure were also observed along with the DOM transformation process of composting. Network analysis further indicated that Caldicoprobacter, Bacillus, and Dechloromonas were associated with the most DOM subcategories. Caldicoprobacter could degrade carbohydrates, Bacillus accelerated the humification by transforming N-containing compounds, and Dechloromonas could degrade polycyclic aromatic hydrocarbons distributed in low O/C. These findings are helpful for understanding the molecular mechanisms of DOM transformation and humification of sludge composting.

Microbial succession and molecular ecological networks response to the addition of superphosphate and phosphogypsum during swine manure composting

This study assessed the effects of superphosphate (SPP) and phosphogypsum (PPG) on the bacterial and fungal community succession and molecular ecological networks during composting. Adding SPP and PPG had positive effects on the bacterial richness and diversity, negative effects on the fungal richness and diversity. The microbial diversity and richness were higher in PPG than SPP. Non-metric multidimensional scaling analysis clearly separated SPP and PPG from the control treatment with no additives. The dominant genera comprised Turicibacter, Bacillus, norank_o_SBR1031, Thermobifida, norank_f_Limnochordaceae, Truepera, Thermopolyspora, Mycothermus, Dipodascus, Thermomyces, and unclassified_p_Ascomycota. In all treatments, the major bacterial species differed clearly in the later thermophilic, cooling, and maturation composting stages, whereas the main fungal species varied significantly in the thermophilic stage. The changes in the dominant microorganisms in SPP and PPG may have inhibited or promoted the degradation of organic matter during various composting stages. Adding SPP and PPG led to more complex bacterial networks and less complex fungal networks, where SPP had more adverse effects on the fungal networks than PPG. SPP and PPG could potentially alter the co-occurrence patterns of the bacterial and fungal communities by changing the most influential species. SPP and PPG changed the composition and succession of the microbial community by influencing different physiochemical properties during various composting stages where the pH was the main explanatory factor. Overall, this study provides new insights into the effects of SPP and PPG on the microbial community and its interactions during composting.

A compost-derived thermophilic microbial consortium enhances the humification process and alters the microbial diversity during composting

This work was conducted to assess the influence of a compost-born multifunctional thermophilic microbial consortium (CTMC) on the physico-chemical parameters, organic matter (OM) transformation and dynamic succession of microbial communities in dairy manure-sugarcane leaves co-composting. The results revealed that CTMC inoculation not only improved the bio-degradation of OM and lignocellulose but also distinctly enhanced the aromaticity and stability degrees of dissolved organic matter and humic substance (HS). Additionally, the complexity and diversity of bacterial and fungal community increased after inoculation. Redundancy analysis indicated that the microbial communities compositions and the physico-chemical parameters interacted with each other in humification process. The dominated bacterial and fungal species related to lignocellulose degradation and humification process were also detected. Accordingly, this research could put forward a possible optimized inoculation strategy to enhance the mineralization of organic carbon, accelerate the lignocellulose degradation and promote the humification process in solid organic waste composting.

Microbial Community Succession and Response to Environmental Variables During Cow Manure and Corn Straw Composting

In composting system, the composition of microbial communities is determined by the constant change in the physicochemical parameters. This study explored the dynamics of bacterial and fungal communities during cow manure and corn straw composting using high throughput sequencing technology. The relationships between physicochemical parameters and microbial community composition and abundance were also evaluated. The sequencing results revealed the major phyla included Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Actinobacteria, Ascomycota, and Basidiomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Actinomycetales and Sordariomycetes were the indicators of bacteria and fungi in the maturation phase, respectively. Mantel test showed that NO3 --N, NH4 +-N, TN, C/N, temperature and moisture content significantly influenced bacterial community composition while only TN and moisture content had a significant effect on fungal community structure. Structural equation model (SEM) indicated that TN, NH4 +-N, NO3 --N and pH had a significant effect on fungal abundance while TN and temperature significantly affected bacterial abundance. Our finding increases the understanding of microbial community succession in cow manure and corn straw composting under natural conditions.