Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH 4 , which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13 CO 2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13 C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (ϳ20%) than did those in the rhizosphere (ϳ4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. The interaction between plants and microorganisms within the root and in the rhizosphere is complex and poorly understood. Early studies focused on specific plant growth-promoting bacteria (1, 2) and more recently on characterizing the rhizosphere microbial community (3). For example, studies with Arabidopsis thaliana, a model plant species, have shown that the root endophytic microbial communities are highly specific (4, 5). In rice, the microbial communities associated with the rhizosphere and the phyllosphere have been characterized by a metaproteogenomic approach (6), and a metagenomic approach was used to characterize the endophytic root community in rice (7).A variety of factors act to shape the microbial community within the roots and in the rhizosphere, including the volume and nature of carbon substrates transported by the plant to the roots (8) and highly evolved signaling and interaction mechanisms between plants and microbes and the plant immune system (9). Plants actively recruit and sustain microorganisms in the root environment in part by the translocation of organic compounds from the leaves to the roots and into the rhizosphere that serve as growth substrates. In annual plants, this has been shown to account for 30 to 60% of net fixed carbon, 40 to 90% of which is excreted by the root and ultimately sequestered or respired by the root-associated microorganisms (10)....
Max 300 words) 1 Land-use change is a prominent feature of the Anthropocene. Transitions between 2 natural and human-managed ecosystems affect biogeochemical cycles in many ways, but soil 3 processes are amongst the least understood. We used a global meta-analysis (62 studies, 4 1670 paired comparisons) to examine effects of land conversion on soil-atmosphere fluxes of 5 methane (CH 4 ) and nitrous oxide (N 2 O) from upland soils, and explored what soil and 6 environmental factors influenced these effects. Conversion from a natural ecosystem to any 7 anthropogenic land use increased soil CH 4 and N 2 O fluxes by 234 kg CO 2 -equivalents ha -1 y -8 1 , on average. Reverting to natural ecosystems did not fully reverse those effects, even after 9 80 years (except for CH 4 fluxes by -12 µg m -2 h -1 ). In general, neither the type of natural 10 ecosystem that was converted, nor the type of anthropogenic land use it was converted to, 11 affected the magnitude of increase in soil emissions. The exception to this is when natural 12 ecosystems were converted to pastures or croplands (emissions increased by +23 and +5 µg 13 CH 4 m -2 h -1 ). A complex suite of variables interacted to influencing CH 4 and N 2 O fluxes, but 14 availability of soil inorganic nitrogen (i.e. extractable ammonium and nitrate), texture, pH, 15 and microclimate were the strongest mediators of effects of land-use change. Land-use 16 changes in wetter ecosystems resulted in greater CH 4 fluxes, and effects of land-use change 17 on soil nitrate, total organic C, and pH emerged as the greatest drivers of changes in CH 4 18 fluxes. Effects of land-use change on N 2 O fluxes decreased in wetter ecosystems, and the 19 land-use change effect was regulated primarily via changes in soil inorganic N and water 20 content. Understanding the complicated effects of land-use changes on soil-atmosphere CH 4 21 and N 2 O fluxes, and the mechanisms underpinning such emissions, could inform land 22 management actions to mitigate increased greenhouse gas emissions after changing land uses.23
22About 50 years ago, most of the natural wetlands in northeast China, the Sanjiang plain, 23 were converted to either flooded rice fields or to upland soybean fields. After the 24 conversion, natural wetland soils were either managed as artificial wetland or as drained 25 upland resulting in soil microbial community changes. The purpose of our study was to 26 understand how methanogenic microbial communities and their functions had changed in 27 the two different soils upon conversion, and whether these communities now exhibit 28 different resistance/resilience to drying and rewetting. Therefore, we determined function, 29 abundance and composition of the methanogenic archaeal and bacterial communities in two 30 soils reclaimed from a Carex wetland 25 years ago. We incubated the soils under anoxic 31 conditions and measured the rates and pathways of CH 4 production by analyzing 32 concentration and δ 13 C of CH 4 and acetate in the presence and absence of methyl fluoride, 33 an inhibitor of acetoclastic methanogenesis. We also analyzed the abundance of bacterial 34 and archaeal 16S rRNA genes, and of mcrA (coding for a subunit of the methyl coenzyme M 35 reductase) using qPCR. The composition of the archaeal and bacterial 16S rRNA genes was 36 determined by using MiSeq illumina sequencing. Our results showed clear differences in 37 structure and function of methanogenic archaeal communities in rice field soil versus upland 38 soil. Furthermore, in both soils composition of bacteria and archaea changed after artificial 39 drying and became less diverse. The archaeal and bacterial signature species in the two soils 40 were also different. However, functional changes were similar, with rates of CH 4 production 41 and contribution of aceticlastic methanogenesis decreasing upon drying and rewetting in 42 both soils.
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