Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems.

Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient of stochastic versus deterministic assembly processes. Carbon and nutrient cycling multifunctionality, characterized by nine enzymes associated with soil carbon, nitrogen, phosphorous and sulfur cycling, was evaluated and then associated with microbial assembly processes and co-occurrence patterns of vital ecological groups. Our results suggest that strong deterministic processes favour microorganisms with convergent functions (as in the upland agroecosystem), while stochasticity-dominated processes lead to divergent functions (as in the flooded agroecosystem). To benefit agroecosystems services, we speculate that it is critical for a system to maintain balance between its stochastic and deterministic assembly processes (as in the paddy agroecosystem). By doing so, the system can preserve a diverse array of functional traits and also allow for particular traits to flourish. To further confirm this speculation, it is necessary to develop a systematic knowledge beyond merely characterizing general patterns towards the associations among community assembly, composition, and ecosystem functions.

Organic and Inorganic Amendments Shape Bacterial Indicator Communities That Can, In Turn, Promote Rice Yield.

The dynamic patterns of the belowground microbial communities and their corresponding metabolic functions, when exposed to various environmental disturbances, are important for the understanding and development of sustainable agricultural systems. In this study, a two-year field experiment with soils subjected to: chemical fertilization (F), mushroom residues (MR), combined application of chemical fertilizers and mushroom residues (MRF), and no-fertilization (CK) was conducted to evaluate the effect of fertilization on the soil bacterial taxonomic and functional compositions as well as on the rice yield. The highest rice yield was obtained under MRF. Soil microbial properties (microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), urease, invertase, acid phosphatase, and soil dehydrogenase activities) reflected the rice yield better than soil chemical characteristics (soil organic matter (SOM), total N (TN), total K (TK), available P (AP), available K (AK), and pH). Although the dominant bacterial phyla were not significantly different among fertilizations, 10 bacterial indicator taxa that mainly belonged to Actinobacteria (Nocardioides, Marmoricola, Tetrasphaera, and unclassified Intrasporangiaceae) with functions of xenobiotic biodegradation and metabolism and amino acid and nucleotide metabolism were found to strongly respond to MRF. Random Forest (RF) modeling further revealed that these 10 bacterial indicator taxa act as drivers for soil dehydrogenase, acid phosphatase, pH, TK, and C/N cycling, which directly and/or indirectly determine the rice yield. Our study demonstrated the explicit links between bacterial indicator communities, community function, soil nutrient cycling, and crop yield under organic and inorganic amendments, and highlighted the advantages of the combined chemical and organic fertilization in agroecosystems.

The Long-Term Effects of Using Phosphate-Solubilizing Bacteria and Photosynthetic Bacteria as Biofertilizers on Peanut Yield and Soil Bacteria Community.

Microbial inoculation is a promising strategy to improve crop yields and reduce the use of chemical fertilizers, thereby creating environment-friendly agriculture. In this study, the long-term (5 years) effects of a phosphate-solubilizing bacterium Burkholderia cepacia ISOP5, a purple non-sulfur bacterium Rhodopseudomonas palustris ISP-1, and a mixed inoculation of these two bacteria (MB) on peanut yield, soil microbial community structure, and microbial metabolic functions were evaluated in a field experiment. After 5 years of inoculation, total peanut yield with B. cepacia ISOP5, R. palustris ISP-1, and MB treatments increased by 8.1%, 12.5%, and 19.5%, respectively. The treatments also significantly promoted the absorption of N and increased the protein content in peanut seeds. Nutrient content also increased to some extent in the bacteria-inoculum-treated soil. However, bacterial community diversity and richness were not significantly affected by bacterial inoculums, and only minor changes occurred in the bacterial community composition. Functional prediction revealed that bacterial inoculums reduced the relative abundance of those genes associated with P uptake and transport as well as increased the abundance of genes associated with inorganic P solubilization and organic P mineralization. Bacterial inoculums also increased the total relative abundance of genes associated with N metabolism. In addition to developing sustainable and eco-friendly agricultural practice, crop inoculation with B. cepacia ISOP5 and R. palustris ISP-1 would improve soil fertility, enhance microbial metabolic activity, and increase crop yield.

Organic matter- and temperature-driven deterministic assembly processes govern bacterial community composition and functionality during manure composting.

Although many studies have shown that microbial communities play important roles in organic waste composting due to the involvement of specific microbial taxa with metabolic functions, the underlying ecological processes of community assembly and governing factors remain elusive. Thus, a chicken manure composting experiment as a model system of microbially mediated organic waste composting was conducted. Ecological null modeling and metabolic functional prediction combined with electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to quantify assembly processes governing bacterial community composition and functions during composting. The results showed the predominant role of deterministic assembly processes in shifting community compositions both across and within composting stages. Stochastic assembly processes also concomitantly influenced microbial community compositions. Changes in the organic matter (OM) content and its chemical properties and temperature governed bacterial community assembly processes throughout the stages by selecting specific bacterial taxa such as Cardiobacteriales, Bacteroidales, and Lachnospiraceae on day 1, Firmicutes on days 6, 25 and 37, and Sphingobacteriales, Thermoactinomycetaceae, Actinobacteria, and Novibacillus on day 45. These taxa ultimately influenced community functions such as environmental information processing, carbohydrate and amino acid metabolism, cellular processes, and genetic information processes involved in composting. Taken together, this study indicates that deterministic assembly processes governed by OM content and quality as well as temperature influenced microbial community turnover and determined community functions during composting. These results are important for better understanding and predicting microbial-driven composting and for ultimately manipulating microorganisms for environmentally-friendly composting outcomes.