It has been documented that human activities are causing the rapid loss of taxonomic, phylogenetic, genetic and functional diversity in soils. However, it remains unclear how modern intensive rice cultivation impacts the soil microbiome and its functionality. Here we examined the microbial composition and function differences between a buried Neolithic paddy soil and an adjacent, currently-cultivated paddy soil using high throughput metagenomics technologies. Our results showed that the currently cultivated soil contained about 10-fold more microbial biomass than the buried one. Analyses based on both 16S rRNA genes and functional gene array showed that the currently cultivated soil had significantly higher phylogenetic diversity, but less functional diversity than the buried Neolithic one. The community structures were significantly different between modern and ancient soils, with functional structure shifting towards accelerated organic carbon （C） degradation and nitrogen （N） transfor- mation in the modem soils. This study implies that, modern intensive rice cultivation has substantially altered soil microbial functional structure, leading to functional homogenization and the promotion of soil ecological functions related to the acceleration of nutrient cycling which is necessary for high crop yields.
为了探明水稻土落干过程对温室气体排放和反硝化微生物的影响,通过模拟水稻土淹水落干过程,系统监测了落干开始后24 h内N2O的释放和氧化还原电位(Eh)的变化,并利用实时PCR(qPCR)方法测定了反硝化功能基因narG和nosZ的丰度.结果表明:落干开始后4 h N2O释放量就明显增加,在24 h时N2O的释放量比淹水对照增加了5倍多;narG和nosZ基因丰度也随着落干过程的推移而快速增加;而且N2O排放通量与narG基因呈极显著相关(P<0.01).表明水稻土短期淹水落干过程中,含narG基因反硝化微生物是驱动N2O释放的主要功能微生物.
Nitrification inhibitors, such as dicyandiamide （DCD）, have been shown to decrease leaching from urea- and ammoniumbased fertilizers in agricultural soils. The effect of nitrification inhibitors on nitrifier and denitrifier in short- and long-term intensive vegetable cultivation soils was poorly understood. In this study, the pot trial was conducted to investigate the differential responses of nitrifier （amoA-containing bacteria） and denitrifier （nirK-containing bacteria） to DCD in short-（soil S） and long-term （soil L） intensive vegetable cultivation soils. Quantitative polymerase chain reaction （qPCR） and terminal restriction fragment length polymorphism （T-RFLP） were employed to detect the abundance and composition of amoA- and nirK-containing communities. The results indicated that application of DCD led to a consistently higher NH4＋-N concentration during the whole incubation in soil L, while it was quickly decreased in soil S after 21 days. Furthermore, DCD induced more severe decrease of the abundance of amoA-containing bacteria in soil L than in soil S. However, the abundance of the nirK- containing community was not significantly affected by DCD in both soils. Long-term vegetable cultivation resulted in a super-dominant amoA-containing bacteria group and less divergence in soil L compared with soil S, and DCD did not cause obvious shifts of the composition of ammonia-oxidising bacteria （AOB）. On the contrary, both amoA- and nirK-containing bacterial compositions were influenced by DCD in soil S. The results suggested that long-term intensive vegetable cultivation with heavy nitrogen fertilization resulted in significant shifts of AOB community, and this community was sensitive to DCD, but denitrifiers were not clearly affected by DCD.
Soil is an essential part of the critical zone,and soil-microbe-plant system serves as a key link among lithosphere,biosphere,atmosphere and hydrosphere.As one of the habitats with the richest biodiversity,soil plays a critical role in element biogeochemistry on the earth surface(weathered crust).Here we review the soil biological processes that are relevant to mineral weathering,element cycling,and transformation,with an emphasis on rock weathering mediated by soil microbes,plant root and the rhizosphere.
Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown. Potential H2-dependent Fe（III）-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor. Terminal restriction fragment length polymorphism （T-RFLP） analysis and cloning/sequencing were conducted to reveal bacterial community structure. Results showed that Geobacter and Clost^dium were the dominant bacteria in the enrichment cultures. Fe（III） oxide mineral phases showed a strong effect on the community structure; Geobaeter and Clostridium were dominant in the ferrihydrite treatment, while Glostridium spp. were dominant in the goethite treatment. These suggested that H2-dependent Fe（lII）-redueing bacteria might be widely distributed in paddy soils and that besides Geobacter, Clostmdium spp. might also be an important group of H2-dependent Fe（III）-reducing microorganisms.
