Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

Sex-induced alterations in rumen microbial communities and metabolite profiles: implications for lamb body weight

BACKGROUND

Microbiota-metabolome interactions play a crucial role in host physiological regulation and metabolic homeostasis. The aim of this study was to investigate that sex induces alterations in rumen microbial community composition and metabolite profiles in lambs and the influence on body weight. This study aimed to demonstrate that sex- induced alterations in rumen microbial community and metabolite profiles and blood indices and their linkage to growth performance in lambs.

RESULTS

This study examined (growth indices, serum indices, rumen fermentation parameters, rumen fluid microbiota community and metabolome profiles) in 180 Hu lambs (90 males, and 90 females) with the same age and diet. At six months, male lambs showed significantly greater body weight, serum indices (glutamic pyruvic transaminase, glutamic oxalacetic transaminase, growth hormone, glucagon-like peptide 1, and ghrelin), and molar percentage of propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid compared to female. However, male had lower VFA molar concentrations (acetic acid, propionic acid, butyric acid, and TVFAs), acetic acid/propionic acid, and VFA molar percentage (acetic acid) than female. Significant sex-related differences were observed in rumen microbiota and metabolic enrichment between genders. Moreover, compared with the females lambs, the relative abundance of Succiniclasticum, uncultured_rumen_bacterium, NK4 A214_group, Veillonellaceae_UCG_001 and Butyrivibrio in the male lambs has been significantly increased, while the relative abundance of Prevotella has been significantly decreased (P < 0.05). Notably, there were significant rumen microbiota-metabolite interactions, especially Firmicutes and Bacteroidota as dominant phyla in the sheep rumen with significant differences in correlation with rumen metabolic modules. Additionally, there are pronounced correlations among the microbiota, particularly within the Firmicutes phylum. Furthermore, the up-regulated metabolites in the rumen fluid of male lambs were predominantly enriched in the amino acid metabolite pathway, and these metabolites exhibited a significant positive correlation with body weight. However, the metabolites that were up-regulated in ewe lambs were predominantly enriched in the lipid metabolic pathway, and these metabolites exhibited a significant negative correlation with body weight. Moreover, lamb rumen microbial markers (Lachnospiraceae_UCG_008, Saccharofermentans, unclassified_Clostridia, Christensenellaceae_R_7_group, Anaerovorax, Mogibacterium, and unclassified_Erysipelotrichaceae) and metabolic markers (C75, 4-Coumarate, Flibanserin,3-Amino-5-mercapto-1,2,4-triazole, 1,3-Propane sultone, Fingolimod phosphate ester, S-,) were significantly positively correlated with body weight, but lamb rumen microbial markers (Anaeroplasma, unclassified_Acholeplasmataceae, uncultured_rumen_bacterum_4c28 d_15) and metabolic markers (Mozenavir, Reduced riboflavin, PG(18:2(9Z,12Z)/0:0), Cowanin) were significantly negatively correlated body weight.

CONCLUSIONS

This study shows that sex-induced alterations in rumen microbial communities and metabolite profiles, adapting to the growth and development of lambs. The findings may help develop targeted strategies to optimize sheep rumen microbiota and improve productivity.

Decomposing the molecular complexity and transformation of dissolved organic matter for innovative anaerobic bioprocessing

The sustainable transformation and management of dissolved organic matter (DOM) are crucial for advancing organic waste treatment towards resource-oriented processes. However, the intricate molecular complexity of DOM poses significant challenges, impeding a comprehensive understanding of the underlying biochemical processes. Here, we focus on the chemical "dark matter" mining using ultra-high resolution mass spectrometry technologies to elucidate the molecular diversity and transformation in anaerobic bioprocessing of food waste. We developed an analytical framework that reveals the persistence of DOM in the final effluent is mainly determined by its molecular properties, such as carbon chain length, aromaticity, unsaturation, and redox states. Our in-depth characterization and quantitative analysis of key biochemical reactions unveils the evolution of DOM composition, providing valuable insights into the targeted conversion of persistent molecules toward full utilization. Additionally, we establish a correlation between the redox state and energy density of a broad range of DOM molecules, enabling us to comprehend and evaluate their biodegradability. These insights enhance the mechanistic understanding of DOM transformation, guiding the rational design and regulation of sustainable organic waste treatment strategies.

Soil-dependent responses of bacterial communities, phosphorus and carbon turnover to uranium stress in different soil ecosystems

Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg-1) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.

The Same Source of Microbes has a Divergent Assembly Trajectory Along a Hot Spring Flowing Path

Hot spring microbial mats represent intricate biofilms that establish self-sustaining ecosystems, hosting diverse microbial communities which facilitate a range of biochemical processes and contribute to the structural and functional complexity of these systems. While community structuring across mat depth has received substantial attention, mechanisms shaping horizontal spatial composition and functional structure of these communities remain understudied. Here, we explored the contributions of species source, local environment and species interaction to microbial community assembly processes in six microbial mat regions following a flow direction with a temperature decreasing from 73.3°C to 52.8°C. Surprisingly, we found that despite divergent community structures and potential functions across different microbial mats, large proportions of the community members (45.50%-80.29%) in the recipient mat communities originated from the same source community at the upper limit of temperature for photosynthetic life. This finding indicated that the source species were dispersed with water and subsequently filtered and shaped by local environmental factors. Furthermore, critical species with specific functional attributes played a pivotal role in community assembly by influencing potential interactions with other microorganisms. Therefore, species dispersal via water flow, environmental variables, and local species interaction jointly governed microbial assembly, elucidating assembly processes in the horizontal dimension of hot spring microbial mats and providing insights into microbial community assembly within extreme biospheres.

Root exudates and microbial metabolites: signals and nutrients in plant-microbe interactions

Plant roots meticulously select and attract particular microbial taxa from the surrounding bulk soil, thereby establishing a specialized and functionally diverse microbial community within the rhizosphere. Rhizosphere metabolites, including root exudates and microbial metabolites, function as both signals and nutrients that govern the assembly of the rhizosphere microbiome, playing crucial roles in mediating communications between plants and microbes. The environment and their feedback loops further influence these intricate interactions. However, whether and how specific metabolites shape plant-microbe interactions and facilitate diverse functions remains obscure. This review summarizes the current progress in plant-microbe communications mediated by chemical compounds and their functions in plant fitness and ecosystem functioning. Additionally, we raise some prospects on future directions for manipulating metabolite-mediated plant-microbe interactions to enhance crop productivity and health. Unveiling the biological roles of specific metabolites produced by plants and microbes will bridge the gap between fundamental research and practical applications.

Rethinking the biochar impact on the anaerobic digestion of food waste in bench-scale digester: Spatial distribution and biogas production

The improvement of biogas production in anaerobic digestion (AD) by biochar introduction has been demonstrated. However, the distribution of biochar in the digester and its effect on AD have been seldom explored. In this study, the distribution of biochar and their impact on AD were investigated in a 30 L semi-continuously operated bench-scale anaerobic digester. The results demonstrated that the biochar significantly increased biogas yields by 23.38 % under an organic loading rate (OLR) of 3.0 g VS/L·d. The stability of the AD under an OLR of 4.0 g VS/L·d was also improved by biochar introduction. The increased stirring speed of the digester enhanced the spatial distribution uniformity of biochar and increased biogas production by 5.89 %. Reducing the particle size of biochar improved its spatial distribution uniformity but did not significantly increase biogas production, likely due to excessive microbial accumulation on the biochar, which have caused substrate competition. Biochar aided AD by boosting microbial genera of Syntrophomonas, Bacteroidota, Cloacimonadot, and Methanosaeta, accelerating volatile fatty acids consumption, and improving microorganisms' spatial ecological niches. The economic analysis showed that applying residue-based biochar for biogas production presented superior benefits and greater development potential than residue incineration in the food waste AD process. Overall, this study presented a novel and comprehensive understanding of the biochar distribution and impact on food waste AD in digesters.

Developing a microfluidic-based epicPCR reveals diverse potential hosts of the mcrA gene in marine cold seep

Anaerobic methanotrophic (ANME) microbes play a crucial role in the bioprocess of anaerobic oxidation of methane (AOM). However, due to their unculturable status, their diversity is poorly understood. In this study, we established a microfluidics-based epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) to fuse the 16S rRNA gene and mcrA gene to reveal the diversity of ANME microbes (mcrA gene hosts) in three sampling push-cores from the marine cold seep. A total of 3725 16S amplicon sequence variants (ASVs) of the mcrA gene hosts were detected, and classified into 78 genera across 23 phyla. Across all samples, the dominant phyla with high relative abundance (>10%) were the well-known Euryarchaeota, and some bacterial phyla such as Campylobacterota, Proteobacteria, and Chloroflexi; however, the specificity of these associations was not verified. In addition, the compositions of the mcrA gene hosts were significantly different in different layers, where the archaeal hosts increased with the depths of sediments, indicating the carriers of AOM were divergent in depth. Furthermore, the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria, suggesting the horizontal transfer of the mcrA gene may occur among host members. Finally, some bacterial metagenomes were found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway, which prospectively propose the existence of ANME bacteria. This study describes improvements for a potential method for studying the diversity of uncultured functional microbes and broadens our understanding of the diversity of ANMEs.

Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge

This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.

Different patterns of bacterioplankton in response to inorganic and organic phosphorus inputs in freshwater lakes - a microcosmic study

Phosphorus (P) is a limiting factor in fresh waters and is also the main cause of water eutrophication and deterioration, However, the practical effect of elevated P level on bacterioplankton is less evaluated. In this study, we investigated the bacterioplankton in a 96 hours microcosm experiment with P additions in two forms (organic/inorganic P, OP/IP) and three levels (final conc., 0.040, 0.065 and 0.125 g/L), aiming to find out the response pattern of bacterioplankton in coping with the increasing P levels. Results showed a more dramatic change of water properties and bacterioplankton between P forms (OP and IP) than among the addition levels, and a more remarkable effect of OP addition than the IP. Both OP and IP treatments significantly decreased the water pH, dissolved oxygen (DO), Electrical Conductivity (EC), Nitrate Nitrogen (NO3--N) and Total Organic Carbon (TOC), and reduced the α-diversity of bacterioplankton and relative abundance of Cyanobacteria, but increased the abundance of Proteobacteria. The IP addition decreased Actinobacteria abundance (especially for HgcI) and showed higher denitrification potentials, while the OP addition depressed the Bateroidota and exhibited lowed methylotrophic functions, but such trends decreased with increasing addition concentrations. The network analysis showed that both IP and OP additions increased the proportion of positively correlated edges and reduced the network complexity and stability, but the OP network was more stable than the IP network. The study clarifies the response pattern of bacterioplankton to the P input with different forms and levels, and deepens our understanding of the eutrophication process, which provides a scientific basis for the management and control of freshwater lakes facing eutrophication.