Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment. 

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

Microbial communities are shaped by the complex interactions among organisms and the environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the complexity and ecological properties of various microbial communities, revealing their intricate interactions. Many researchers have modified GEMs for the microbial communities based on specific needs. Thus, GEMs need to be comprehensively summarized to better understand the trends in their development. In this review, we summarized the key developments in deciphering and designing microbial communities using different GEMs. A timeline of selected highlights in GEMs indicated that this area is evolving from the single-strain level to the microbial community level. Then, we outlined a framework for constructing GEMs of microbial communities. We also summarized the models and resources of static and dynamic community-level GEMs. We focused on the role of external environmental and intracellular resources in shaping the assembly of microbial communities. Finally, we discussed the key challenges and future directions of GEMs, focusing on the integration of GEMs with quorum sensing mechanisms, microbial ecology interactions, machine learning algorithms, and automatic modeling, all of which contribute to consortia-based applications in different fields. 

Deciphering and designing microbial communities by genome-scale metabolic modelling

Water contamination with heavy metals seriously affects water and sediment quality and may affect the aquatic biota. This study assessed the impact of heavy metals on the morphological characteristics of aquatic microorganisms in potentially contaminated water. Different physicochemical parameters and heavy metals contents were analyzed for toxicological assessment along with microbial diversity in the rivers Swat and Kabul. The pH of River Swat water was neutral to slightly alkaline, while River Kabul was neutral to slightly acidic. The results showed substantial variations in heavy metal concentration across different sampling points. In both River Swat and River Kabul water samples, Cu and Zn concentrations were below the permissible limits for surface and drinking water qualities while the rest of the heavy metals exceeded the permissible limit with Cd being the most abundant heavy metal. Similarly, in sediment samples all the heavy metals were below the permissible limits except for Cd that exceeded the Environment Canada (EC) limits in River Swat and EC and NOVA limits in River Kabul. The rest of the heavy metals concentrations were within the permissible limits, with few exceptions. The results showed that in River Swat, most of the contamination was of geogenic origin, while the main source of contamination in River Kabul was anthropogenic. Results of microbial analysis showed that River Swat has more diversity than River Kabul, which may be due to the low contamination profile of River Swat. It was further observed that high heavy metal concentrations negatively impact the morphological characteristics of microorganisms. The heavy metals concentration and microbial diversity were closely related to each other.

Heavy Metals and Microbial Diversity: A Comparative Analysis of Rivers Swat and Kabul

Understanding the developmental characteristics of microbial communities in biofilms is crucial for designing targeted functional microbial enhancements for the remediation of complex contamination scenarios. The strong prioritization effect of microorganisms confers the ability to colonize strains that arrive first dominantly. In this study, the auto-aggregating denitrifying bacterial Pseudomonas stutzeri strain YC-34, which has both nitrogen and chromium removal characteristics, was used as a biological material to form a stable biofilm system based on the principle of dominant colonization and biofortification. The effect of the biofilm system on nitrogen and chromium removal was characterized by measuring the changes in the quality of influent and effluent water. The pattern of biofilm changes was analyzed by measuring biofilm content and thickness and characterizing extracellular polymer substances (EPS). Further analysis of the biofilm microbiota characteristics and potential functions revealed the mechanism of strain YC-34 biofortified biofilm. The results revealed that the biofilm system formed could achieve 90.56% nitrate-nitrogen removal with an average initial nitrate-nitrogen concentration of 51.9 mg/L and 40% chromium removal with an average initial hexavalent chromium Cr(VI) concentration of 7.12 mg/L. The biofilm properties of the system were comparatively analyzed during the biofilm formation period, the fluctuation period of Cr(VI)-stressed water quality, and the stabilization period of Cr(VI)-stressed water quality. The biofilm system may be able to increase the structure of hydrogen bonds, the type of protein secondary structure, and the abundance of amino acid-like components in the EPS, which may confer biofilm tolerance to Cr(VI) stress and allow the system to maintain a stable biofilm structure. Furthermore, microbial characterization indicated an increase in microbial diversity in the face of chromium stress, with an increase in the abundance of nitrogen removal-associated functional microbiota and an increasing trend in the abundance of nitrogen transfer pathways. These results demonstrate that the biofilm system is stable in nitrogen and chromium removal. This bioaugmentation method may provide a new way for the remediation of heavy metal-polluted water bodies and also provides theoretical and application parameters for the popularization and application of biofilm systems. 

Enhanced chromium and nitrogen removal by constructing a biofilm reaction system based on denitrifying bacteria preferential colonization theory

Maize is one of the major crops cultivated in northern Shandong Province and contributes significantly to China's maize production, and nitrogen (N) application to the soil can have a marked impact on maize yield and soil microbial productivity. The current environmental challenge, which needs urgently to be addressed, is to effectively utilize fertilizer nitrogen to improve crop production without causing environmental stress in sustainable agroecosystems. Soil fungi can improve plant health and crop performance through improved nutrient uptake and reducing plant stress levels. How soil N influences fungal diversity and maize yield at spatial patterns remains unclear. In this study, the influences of different soil N treatments on maize yields and fungal diversity were investigated in maize fields at five N rates (from 0 to 120 kg ha−1). High-throughput sequencing of the internal transcribed spacer (ITS) region revealed that α- and β-diversities of fungi significantly increased at 80 kg N ha−1 (N80) but decreased significantly in the control (N0) and other N treatments. Variations in the NC model predicted strong fungal distribution patterns (R2 = 0.60) among all the treatments. The highest proportion of operational taxonomic units (OTUs) (68.99%) was observed at N80. The study also found that the complexity of the co-occurrence network significantly stabilized at N80, but a decrease in network complexity was observed at N120. The study showed that, relative to the control, the addition of N to the soil significantly increased the abundance of Ascomycota at the phylum level and Chaetomium, Fusarium, and Mortierella at the genus levels, with average abundances of 5.82%, 1.67%, and 19.58%, respectively. Functional ecology analysis indicated that soil N upregulated the composition of ecological fungal communities by stochastic processes. The composition of major fungal sub-communities was positively correlated with nitrogen/carbon cycling at N80. Moreover, results also indicated that the yields (3.14 t ha−1) and other agronomic effects at N80 were significantly higher than those in the other treatments. This study demonstrates that optimal nitrogen application achieves increases in both fungal diversity and yield, contributing to improved crop production and sustainability at spatial scales. 

Impact of nitrogen fertilizer application on soil fungal diversity and maize yield variation in Shandong Province, China

Spatial distribution patterns across multiple microbial taxonomic groups.

ABSTRACT The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with Xathomonas sacchari JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa, Bacillus, Azospira, Azospirillum, and Arthrobacter, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments. IMPORTANCE Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant’s ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding. Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant’s ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.

Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages

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Spatial distribution patterns across multiple microbial taxonomic groups.

Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages