Amidst the escalating issues of water eutrophication and water resource scarcity, the development of high-efficiency wastewater treatment technologies has become increasingly imperative. Traditional nitrogen and phosphorus removal processes face challenges in achieving efficient simultaneous elimination of nitrogen and phosphorus due to the disparities in sludge age and the competition for carbon sources among microorganisms. Denitrifying phosphorus-accumulating organisms (DPAOs) possess the capability to remove both nitrogen and phosphorus, demonstrating significant potential in wastewater treatment. However, population-level studies often overlook cellular heterogeneity, leading to an inadequate understanding of the nitrogen and phosphorus removal mechanisms of DPAOs. Moreover, the “traditional culture-first, screen-second” method yields a limited number of efficient DPAO strains, the stability and adaptability of which face challenges in actual wastewater treatment environments. Single-cell analysis technologies provide new perspectives for a deeper understanding of microbial ecological niches and metabolic mechanisms. Coupling non-destructive single-cell phenotypic identification technologies, such as single-cell Raman spectroscopy (SCRS), with the culture method paves new avenues for the exploration of DPAO strains. This review summarizes the research status and progress in the exploration of DPAO strain resources and their metabolic mechanisms, focusing on the potential of single-cell technologies in revealing the mechanisms of nitrogen and phosphorus removal by DPAOs and in the exploration of DPAO resources. The aim is to provide a new theoretical foundation and technical support for the research and application of DPAOs, thereby promoting the development of efficient wastewater treatment technologies.

Soybean (Glycine max) is an important cereal and oil crop in the world, and the supply-side structural reform in the agricultural sector requires an increase in the planting area of high-quality edible soybean. Due to the inherent characteristics of arable land resources in China, the domestic production of soybean is far from self-sufficiency, and there is an urgent need to increase the planting area and production of soybean domestically, reducing the dependence on imports. Rhizobia are the earliest developed microbial fertilizer, while their application area is limited in China. [Objective] To select suitable strains from the stored rhizobia to provide germplasm resources for alleviating food issues. [Methods] We reviewed taxonomic status of rhizobia preserved in the Agricultural Culture Collection of China over decades based on the 16S rRNA and recA gene sequences. The hydroponic nodulation test was carried out to assess the nodulating and soybean growth-promoting effects based on comprehensive consideration of the nodulation rate, nodule number, nodule weight, plant height, and dry weight. [Results] A total of 213 strains of soybean rhizobia were activated and identified, including 156 strains of Bradyrhizobium, 48 strains of Sinorhizobium, and 9 strains of Rhizobium. Among them, 149 strains were able to nodulate with soybean cultivar selected in this study, and 43 strains significantly contributed to the growth of soybean plants. [Conclusion] This study further clarifies the taxonomic status of preserved soybean rhizobia and evaluates their nodulating and plant growth-promoting effects, providing abundant microbial resources for the development of soybean rhizobia-based agents.

The preservation and utilization of agricultural microbial resources are essential for achieving green and sustainable agricultural development in China. However, the current state of agricultural microbial resources in China is characterized by a limited total volume, insufficient characterization data, low preservation throughput, poor development, and low sharing efficiency. Establishing and operating advanced agricultural microbial resource repositories can provide high-quality resources for the development of innovative microbial agricultural products and ensure robust sharing of agricultural microbial resources. Based on the construction and operation experience of conventional microbial resource repositories and considering the trends of scientific development in the new era, this paper proposes several insights into the construction and operation of new agricultural microbial resource repositories as a reference for resource repository developers and managers.

Aureobasidium spp. are a group of fungi with remarkable ecological adaptability and stress tolerance. They are ubiquitous in natural environments such as plants and can survive under extreme conditions. The genomes of Aureobasidium spp. show specific differentiation characteristics, and the strains have obviously advantage characteristics in fermentation. Aureobasidium spp. can utilize a broad spectrum of carbon sources and produce a rich variety of metabolites. Aureobasidium spp. and their metabolites have significant application potential in fields such as biomedicine, biocontrol, and food processing. This article introduces the distribution, classification, main metabolites, and multidisciplinary applications of Aureobasidium spp. In the future, with the advancement in multidisciplinary fields such as genome editing and intelligent biomanufacturing, Aureobasidium spp. are expected to play an important role in biomanufacturing and sustainable development industries.

Edible forest mushrooms are one of the main forest foods and an essential resource for forests to achieve the functions of conserving water, bringing in economic benefits, boosting grain production, and also serving as a carbon sink. This study summarizes the current situation of the edible forest mushroom industry in China, such as benign development with imbalanced regional development, scaled planting under forests but lack of regional characteristics and deep processing products, and the advantages of edible ectomycorrhizal mushrooms with weak scientific and technological support. Suggestions are put forward on optimizing planning, promoting the investment of scientific and technological resources, accelerating digital intelligence and multi-mode development, conducting climate change monitoring, and protecting germplasm resources, in order to make positive contributions to the development of the edible forest mushroom industry and provide scientific and technological support for the practice of the big food concept.

[Objective] To explore the effects of endophytic bacteria in soybean nodules on the growth of soybean seedlings under salt stress and provide reference for the high-quality development of crops in the Yellow River Basin. [Methods] A pot experiment was conducted with the soybean cultivar ‘Xudou 20’ under artificial climate conditions. Three groups were designed: control, salt stress, and salt stress inoculated with endophytic bacteria. The growth of soybean seedlings in each group was measured. [Results] Regarding strain 72, in the case of inoculation with the suspension at OD₆₀₀=0.75 (2:1) and the salt concentration of 200 mmol/L, the activity of catalase (CAT) in the seedlings of 21 days was the highest (2.010 0 U/g FW), which was 54.02% higher than that in the salt stress group; in the case of inoculation with the suspension at OD₆₀₀=0.33 (1:2) and the salt concentration of 300 mmol/L, the proline content was the highest (0.028 6 mg/g); in the case of inoculation with the suspension at OD₆₀₀=0.75 (2:1) and the salt concentration of 100 mmol/L, the proline content was 64.38% higher than that in the salt stress group. Regarding strain 146, the seedlings of 21 days in the case of inoculation with the suspension at OD₆₀₀=0.50 (1:1) and the salt concentration of 50 mmol/L had the highest CAT activity (1.350 0 U/g FW); the seedlings of 28 days in the case of inoculation with the suspension at OD₆₀₀=0.75 (2:1) and the salt concentration of 100 mmol/L had the CAT activity 272.73% higher than that in the salt stress group; the seedlings in the case of inoculation with the suspension at OD₆₀₀=0.75 (2:1) and the salt concentration of 150 mmol/L had the highest proline content of 0.147 0 mg/g, which was 860.78% higher than that in the salt stress group. The results indicated that inoculation with the endophytic bacterial strain 72 or 146 had a repairing effect. The increases in the CAT activity and proline content in the soybean seedlings inoculated with strain 146 over those in the salt stress group were generally higher than those in the case of inoculation with strain 72, indicating that the repairing effect of strain 146 was more obvious. The phylogenetic tree built based on 16S rRNA gene sequences showed that strains 72 and 146 had the highest similarity with Bacillus subtilis (99.45%) and B. protolyticus (100%), respectively. [Conclusion] Inoculating endophytic bacteria was of great significance for alleviating the effect of saline-alkali stress in the Yellow River Basin on the growth of soybean seedlings and developing biological repairing agents.

[Objective] To optimize the anaerobic digestion process for methane production of hulless barley straw with mixed addition of biochar and Fe₃O₄ and investigate the feasibility of mixed addition of biochar and Fe₃O₄ in the anaerobic digestion of lignocellulosic waste. [Methods] We employed single factor and response surface experiments to optimize the anaerobic digestion process for methane production of hulless barley straw with mixed addition of biochar and Fe₃O₄. Metagenomics was employed to analyze the microbial community structure and methane production pathway during digestion. [Results] The optimal digestion conditions were 6.32% total solids, biochar-to-Fe₃O₄ ratio of 6.83:3.17, and inoculation ratio (volatile solids ratio of inoculum to hulless barley straw) of 2.51. Under these conditions, the measured value of cumulative methane production based on volatile solids was 269.04 mL/g, with a relative error of less than 5% from the predicted value (265.95 mL/g), which indicated that the model was effective. The mixed addition treatment under the optimized conditions increased the methane production of hulless barley straw (P<0.05), with the effect comparable to that of the chemical pre-treatment. Meanwhile, the treatment increased the acetic acid content while reducing the accumulation of propionic and butyric acids. Metagenomic analysis showed increases in the relative abundance of bacterial taxa such as unclassified_Bacteroidota, unclassified_Bacteria, Clostridium, and Fibrobacter, as well as acetotrophic methanogens such as Methanosarcina and Methanothrix, which promoted the utilization of acetic acid and enhanced the direct interspecies electron transfer (DIET) between microorganisms. The mixed addition of biochar and Fe₃O₄ in the anaerobic digestion system enhanced the acetotrophic methanogenic pathway, thereby enhancing methane production. [Conclusion] The response surface methodology can optimize the anaerobic digestion process for methane production of hulless barley straw with mixed addition of biochar and Fe₃O₄. The mixed addition of biochar and Fe₃O₄ enables efficient production of biomethane and environmentally friendly treatment of lignocellulosic waste.

The fruiting bodies of fungi of genus Shiraia inhabiting bamboo have a medicinal use in traditional Chinese medicine. Hypocrellin A (HA), the main bioactive perylenequinone pigment from S. bambusicola fruiting bodies is a novel non-porphyrin photosensitizer with antitumor and antimicrobial properties. [Objective] To investigate the effects of Shiraia fruiting body-associated fungi on HA biosynthesis and develop a co-culture method for enhancing HA production. [Methods] Shiraia fruiting body-associated fungi were isolated and the strains influencing HA biosynthesis were screened by a plate confrontation assay. The effects of intracellular and extracellular metabolites of the strains on HA production were evaluated. A co-culture system for Shiraia sp. S9 and associated fungi was established and optimized for enhancing HA production. [Results] There were 34 fungal strains including 6 host Shiraia strains isolated from the fruiting bodies. Among them, Fusarium sp. SF12 and its extracellular polysaccharides significantly promoted HA biosynthesis. Fusarium sp. SF12 did not noticeably affect the growth of Shiraia sp. S9 but regulated HA synthesis by upregulating the transcription levels of key enzyme genes involved in HA biosynthesis. The total HA yield was enhanced to 209.46 mg/L on day 8 after adding spores (100 cell/mL) from Fusarium sp. SF12 to the Shiraia culture at the time point of 24 h, which was 1.93 times that of the control. [Conclusion] There are diverse fungi in Shiraia fruiting bodies. The co-culture of the associated fungus Fusarium sp. SF12 and the host Shiraia sp. S9 is a new technique to improve HA production.

[Objective] Chitin lyases are the key enzymes for bacteria to degrade chitin. Pseudoalteromonas arabiensis N1230-9 possesses five chitin lyase-encoding genes (woc28159, woc28160, woc28161, woc27404, and woc27232). Functional identification of these five genes is crucial for determining the ability of strain to degrade chitin. [Methods] The distribution patterns of five chitin lyases from strain N1230-9 in 44 model strains of Pseudomonas were analyzed by bioinformatics methods. The transcription levels of five chitin lyase-encoding genes of strain N1230-9 cultured in the medium with chitin as the sole carbon source were analyzed by RT-qPCR. The mutants with deletion of chitin lyase-encoding genes were constructed by homologous recombination, and their abilities to degrade chitin were evaluated. [Results] Thirty-three Pseudoalteromonas strains possessed chitin lyase homologous proteins of strain N1230-9. Chitin significantly upregulated the transcription levels of woc28159, woc28160, woc28161, and woc27404, and the deletion of each of the four genes weakened the chitin-degradation ability. The transcription level of woc27232 was not affected by chitin, and the deletion of this gene did not affect the chitin-degradation ability of the strain. [Conclusion] WOC28159 and WOC28161 are necessary for the degradation of chitin by strain N1230-9. WOC28160 and WOC27404 endow strain N1230-9 with efficient chitin-degrading ability, while WOC27232 does not participate in the chitin degradation process.

The dinitroaniline herbicide pendimethalin, as a pre-emergent herbicide, is widely employed for weed control in cotton fields across Xinjiang. Characterized by chemical stability, prolonged residual activity, bioaccumulative potential, and biomagnification, it is extensively applied in agricultural practice, leading to increased risks to soil ecosystems. Accordingly, the removal of pendimethalin residues has garnered increasing attention. [Objective] To enrich the microbial consortia with pendimethalin-degrading ability, study succession characteristics of microbial consortia during the enrichment culture process under pendimethalin stress, and identify the key microorganisms involved in pendimethalin degradation. [Methods] The cotton field soil under long-term pendimethalin stress was inoculated into MSM media with pendimethalin at 0, 1.2, and 12 mg/L, respectively. The succession of the microbial consortium structure under pendimethalin stress was investigated by high-throughput sequencing. [Results] Two microbial consortia capable of degrading pendimethalin were enriched. Among them, L4 (low-concentration group) achieved a degradation rate of 100% for 1.2 mg/L pendimethalin within 11 days, while H4 (high concentration group) showed a degradation rate of 37.2% for 12 mg/L pendimethalin over the same period. The alpha diversity of microbial consortia was considerably decreased by pendimethalin stress, and the bacteria responded to the stress more strongly than fungi. The microbial consortium structure varied with different concentrations of pendimethalin. The network stability, complexity, and modularity were diminished by pendimethalin stress. Linear discriminant analysis effect size (LEfSe) results showed that the specific bacterial taxa in the high concentration group were Achromobacter, Leifsonia, Candidatus_Nucleicultrix, Enterobacter, and Chryseobacterium. The specific bacterial taxa in the low concentration group were Methyloversatilis, Pseudoxanthomonas, Ancylobacter, Methylorubrum, Thermomonas, and Pseudoflavitalea. Talaromyces, Trichoderma, Paracremonium, Scedosporium, and Sarocladium were the specific fungal taxa. The PICRUSt2 analysis showed the pendimethalin stress significantly enriched the pathways related to degradation. The correlation analysis between microbial genera and pendimethalin degradation showed that Methylorubrum, Hyphomicrobium, Microbacterium, Rhodopseudomonas, and Fusarium had positive correlations with pendimethalin degradation in the low concentration group. Hyphomicrobium, Leifsonia, Rhodopseudomonas, Talaromyces, and Trichoderma were positively correlated with pendimethalin degradation in the high concentration group. [Conclusion] Two microbial consortia capable of degrading pendimethalin were successfully obtained through enrichment culture under varying concentrations of pendimethalin. Leveraging high-throughput sequencing, this study systematically explored the succession patterns of microbial consortia under pendimethalin stress. Key functional microorganisms associated with pendimethalin degradation were preliminarily identified. The findings provide a theoretical basis for the targeted screening of efficient microbial strains dedicated to pendimethalin degradation.