Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

Abstract

In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

“…Chen et al (2011) [10] also demonstrated that AOA activity Environments 2017, 4, 84 6 of 9 was relatively higher in paddy soils at lower pH. In contrast, a study on paddy soils of varying pH (7.3-8.1) that have been under rice cultivation for 50, 100, 300, 2000 years showed that there was no significant difference for archaeal amoA gene abundance whereas bacterial amoA gene abundance varied significantly [33]. These results also showed that the application of N fertilizer could increase the AOB abundance in paddy soils.…”

Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

“…The removal of sulfide through microbial oxidation is an important geochemical and ecosystem process (1)(2)(3)(4)(5)(6); however, resolving the spatial, functional, and temporal relationships among bacteria that control the oxidative reactions of the sulfur cycle has been hampered by an overreliance on the 16S rRNA gene to serve as a proxy for microbial metabolism. Combining functional gene analysis with 16S rRNA phylogenies (7)(8)(9)(10)(11)(12)(13) can improve the resolution of potential microbially mediated geochemical reactions occurring in the environment. There are several enzymatic systems that have been associated with the oxidation of reduced sulfur compounds (14)(15)(16), with the sulfur oxidation (Sox) system being widespread among photosynthetic and nonphotosynthetic bacteria (14,15,17).…”

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

“…3). Although, real-time PCR has been used to investigate the impact of rice cultivation on N-related genes, and most of these functional genes were elevated (per gram soil) in aged paddy soils [17]; while in the present study, we were able to compare currently cultivated soil with the Neolithic one (thus with minimal input of chemical N fertilizers) using a more comprehensive assay which provided a higher resolution picture of N functional genes. All these results demonstrated that the potential functional activity of microbial communities in currently cultivated paddy soils were significantly different from the buried one.…”

“…Although these studies have increased our knowledge about microbial processes in paddy soils, they represented only a small fraction of microbial community. Recently, changes in abundance and diversity of the functional groups of microbial communities was observed in wetland, and paddy soils with repeated tillage management for different time periods [17].…”