Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China

The type and degree of salinized soils together shape the composition of phoD-harboring bacterial communities, thereby altering the effectiveness of soil phosphorus cycling

Limitations in soil nutrient content, particularly phosphorus (P), are key factors constraining saline soil ecosystems. Soil phosphorus-cycling functional microorganisms contribute to the conversion of insoluble phosphorus and increase available phosphorus (AP) levels in phosphorus-deficient soils. However, there is limited knowledge on how soil phoD-harboring bacterial communities regulate AP availability across varying salinization types and degrees. This work evaluated the diversity, composition, assembly, and co-occurrence network properties of phoD-harboring bacteria, and explored their relationship with AP in salinized soils of Ningxia. First, TP, APi, and Ca10P levels were high in all salinized soils, whereas bioavailable fractions (AP, MBP, Ca2P, and Ca8P) were significantly low, limiting plant phosphorus uptake. Notably, the phoD gene, which is the most abundant functional gene involved in phosphorus cycling in saline soils, exhibits a pronounced salt-stress attenuation pattern along with the Shannon and Chao1 indices of the phoD-harboring bacterial community. Consistent with this pattern, the network complexity and stability of these bacteria were overall negatively affected by saline stress pressure when compared to non-saline soils. Furthermore, as evidenced by the distribution variations among bacteria such as Bradyrhizobium, Skermanella, Pseudomonas, Streptomyces, and Mesorhizobium, the type and degree of salinization jointly shape the composition of soil phoD-harboring bacterial communities. Importantly, the composition of these bacteria communities significantly regulates alkaline phosphatase ALP activity, thereby increasing soil AP levels. Consequently, the type and degree of salinized soil can indirectly regulate AP levels by influencing the composition of the phoD-harboring bacterial community. The research findings highlight that the composition of the phoD-harboring bacteria community is critical for the regulation of phosphorus efficiency in saline-affected soils, which holds significant theoretical and practical implications for the management of phosphorus in salinized soils and sustainable agricultural practices.

Biochar-mediated remediation of low-density polyethylene microplastic-polluted soil-plant systems: Role of phosphorus and protist community responses

While the prevalent utilization of plastic products has enabled social advancement, the concomitant microplastics (MPs) pollution presents a serious threat to environmental security and public health. Protists, as regulators of soil microorganisms, are also capable of responding most rapidly to changes in the soil environment. The amelioration mechanisms of biochar in the soil-plant systems polluted by low-density polyethylene microplastics (LDPE-MPs) and the response of protist communities in the soil-plant systems polluted by MPs remain unclear. In this field experiment, the same concentration of biochar (2 %) was applied to remediate different concentrations (1 % and 10 %) of LDPE-MPs pollution in cherry radish soil. The main results indicate that, when compared with the treatment of applying biochar to address high-level LDPE-MPs polluted soil (BP2), the remediation of low-level LDPE-MPs polluted soil by biochar (BP1) led to a 62.02 % reduction in soil available phosphorus. Meanwhile, the abundance of phoD and the activity of alkaline phosphatase increased by 127.75 % and 22.57 % respectively. Moreover, in contrast to BP2, the root biomass and phosphorus content of cherry radish in BP1 increased by 52.80 % and 42.86 % respectively. For protist communities, their structure, niche width, and assembly were altered. The interaction between biochar and LDPE-MPs influenced phosphorus cycling, and protists were closely associated with these processes. Therefore, soil phosphorus cycling indicators and protist community may be important indicators for biochar amelioration on soil MPs pollution. The study highlights the importance of considering these factors for better farmland management in the context of MPs pollution, which is significant for sustainable agriculture and environmental protection.

Lithology and elevated temperature impact phoD-harboring bacteria on soil available P enhancing in subtropical forests

Plants are generally limited by soil phosphorus (P) deficiency in forest ecosystems. Soil available P is influenced by lithology, temperature, and soil microbes. However, the interactive effects of these factors on soil P availability in subtropical forests remain unclear. To assess their impacts, we measured soil inorganic and available P fractions and the diversity, composition, and co-occurrence network of phoD-harboring bacteria in two contrasting forest soils (lithosols in karst forests and ferralsols in non-karst forests) in the subtropical regions of southwestern China across six temperature gradients. The present results showed that the complexities in composition and network and the diversity indices of phoD-harboring bacteria were higher in the karst forest soils than those in the non-karst forest soils, with marked differences in composition. In both types of forest soils, the complexities of composition and networks and the diversity indices were higher in the high-temperature regions (mean annual temperature (MAT) > 16 °C) compared to the low-temperature regions (MAT <16 °C). Soil total inorganic and available P contents were lower in the karst forest soils compared to the non-karst forest soils. Soil total available P contents were lower in the high temperature regions than those in the low temperature regions in both forest soils, whereas soil total inorganic P contents were contrary. Variance partitioning analysis showed that soil inorganic and available P fractions were predominantly explained by lithology and its interaction with soil microbes and climate. The present findings demonstrate that soil P availability in subtropical forests of southwestern China is influenced by lithology and temperature, which regulate the diversity, composition, and network connectivity of phoD-harboring bacteria. Furthermore, this study highlights the significance of controlling the composition of phoD-harboring bacteria for mitigating plant P deficiency in karst ecosystems.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.