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Soil Microbes on Demand: How Soil Microbes are Selected by Ecosystem Needs
Scientists have discovered that soil microbes with functional genes that maintain ideal conditions for ecosystem functions are selected based on ecosystem needs.

The functional gene content of soil microbes is essential in regulating ecosystem functions as they regulate ecological processes like decomposition, nutrient cycling, and plant productivity. However, despite the soil microbes’ importance, not much is known about how they improve the nutrient-stressed environment and retain their abilities to support various ecosystem functions in tropical rainforests.

To better understand the microbial recruitment process and the determining factors that result in their survival and selection in a tropical rainforest ecosystem, spatial mapping of the functional gene content of the soil microbes is essential to study how these variations affect the ecological processes within the ecosystem.

Thus, to gain insights into the spatial pattern of nitrogen (N) and phosphorus (P) cycling functional genes, a team of researchers from the Xishuangbanna Tropical Botanical Garden (XTBG) collected, extracted, and analysed microbial DNA from the soil samples. In particular, the researchers tracked the nitrogen cycle functional genes like NirK, AOA, and AOB – molecular indicators for the presence of ammonia oxidisers and denitrifiers, as well as the phosphorus cycle functional gene PhoD – a molecular indicator used to evaluate the mineralisation of organic phosphorus. Ammonia oxidation and denitrification are both key steps in the nitrogen cycle that control the bioavailable nitrogen content in the soil. Similarly, the mineralisation of organic phosphorus by PhoD gene-containing bacteria is essential to ensure sufficient inorganic phosphate in soil for plant uptake and growth.

The researchers found that the phosphorus cycle-related PhoD functional gene was the most dominant in the Xishuangbanna forest, being the most spatially varied in the most abundant quantities, out of all the other genes studied. The nitrogen cycle-related NirK and AOA genes were less abundant in number and were distributed less widely, followed by the AOB genes.

It was also discovered that the PhoD gene was positively correlated to the stoichiometric ratio between nitrogen and phosphorus in the soil, and it alone was responsible for the increase in plant biomasses observed in the flora. Furthermore, the abundance of the PhoD gene was observed in the presence of phosphorus-poor tropical rainforest soil, so more microbes with this gene were present to ensure sufficient inorganic phosphorus for plant growth and thus, ecosystem flourishing. The researchers concluded that their findings indicated that microbes are recruited in the soil depending on its pre-existing nutrient content as well as the needs of the ecosystem.

“Therefore, in-depth spatial monitoring of microbial functions is required for identifying the microbial mechanisms of performing ecological functions (nutrient cycling, stress resistance, plant productivity, litter decomposition), their adaptation strategies to disturbances such as nutrient limiting conditions, and their contributions (cooperate or compete) to the plant community,” said Yang Xiaodong of XTBG.

Dr. Yang also reflected that his team’s method of studying the relationships between soil microbes’ functional genes and the habitat they exist in may also be further used for keeping track of soil health and observing the wider implications of the soil’s health on ecosystem functioning.

Source: Mishra et al. (2022). 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. Science of the Total Environment, 156863.

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