The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2564 fecal samples from 538 subjects across all interventions.
<p>Ammonium (NH<sub>4</sub><sup>+</sup>) and nitrate (NO<sub>3</sub><sup>&#8211;</sup>) concentrations and production rates in forest soil vary by hillslope position due to variation in ammonia-oxidizing microorganism concentrations, soil chemistry, and surface soil moisture. These spatial distributions have a significant effect on nutrient cycles and streamwater chemistry. Soil moisture conditions significantly restrict microbial activity, influencing the spatial distribution of NO<sub>3</sub><sup>&#8211;</sup> concentrations on forest hillslopes. However, studies linking forest hydrological processes to nitrogen cycling are limited. Therefore, we investigated the determinants of spatial variation in soil moisture and evaluated the effects of soil moisture fluctuations on spatial variation in NO<sub>3</sub><sup>&#8211;</sup> concentration and production rate.</p><p>The study sites were the Fukuroyamasawa Experimental Watershed (FEW) and Oyasan Experimental Watershed (OEW) in Japan. The two have similar topographies, climates, and tree species. In each watershed, a 100 m transect was set up from the ridge to the base of the slope, and soil moisture sensors were installed at soil depths of 10 cm and 30 cm at both the top and bottom of the slope. We collected surface soil samples at a depth of 10 cm at the top, middle, and bottom of the slopes using 100 cm<sup>3</sup> cores, and measured soil physical properties, particle size distribution, volcanic ash content, chemical properties (pH, NO<sub>3</sub><sup>&#8211;</sup>, NH<sub>4</sub><sup>+</sup>, nitrification rate, and mineralization rate), and microbial content (archaeal content). Spatial and temporal changes in soil moisture on the hillslope were calculated using HYDRUS-2D to examine contributing factors of soil moisture.</p><p>At FEW, high NO<sub>3</sub><sup>&#8211;</sup> concentrations and nitrification rates were observed only at the slope bottom and middle, and no NO<sub>3</sub><sup>&#8211;</sup> concentrations were detected at up slope. By contrast, at OEW, high NO<sub>3</sub><sup>&#8211;</sup> concentrations and nitrification rates were observed at all points. NH<sub>4</sub><sup>+</sup> concentrations were similar at all points in both watersheds. At FEW, 10 cm surface soil moisture fluctuated within 25&#8211;40% at the slope top but was within 40&#8211;50% at the slope bottom. At OEW, surface soil moisture was 30&#8211;40% at both the slope top and bottom, with no significant differences according to slope position. It was confirmed that soil moisture was significantly involved in NO<sub>3</sub><sup>&#8211; </sup>concentration and nitrification rates. Model simulations showed that the difference in soil moisture fluctuations between FEW and OEW was mainly explained by the spatial variation in soil physical properties. In particular, volcanic ash influenced soil moisture along the entire slope at OEW, resulting in high water retention, but only influenced soil moisture at the slope bottom at FEW. These findings indicate that spatial variability in soil physical properties has a significant effect on soil moisture fluctuation and leads to a spatial distribution of NO<sub>3</sub><sup>&#8211;</sup> production.</p>
We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.
The measurement of 15N concentrations in environmental samples requires sophisticated pretreatment devices and expensive isotope-ratio mass spectrometry (IRMS). This report describes the use of a gas chromatograph equipped with a quadrupole-type mass spectrometer (GC/MS) to measure 15N concentrations of ammonium, nitrate, nitrite, and total dissolved nitrogen (TDN) in distilled water, a 2 M KCl solution and a 0.5 M K2SO4 solution. The system measures nitrous oxide (N2O) that is ultimately converted from the target N compound, requiring no special apparatus such as a purge-and-trap pretreatment device. It uses a denitrifier lacking N2O reductase, which produces N2O from nitrate. Persulfate oxidation was applied to convert TDN to nitrate, while additional pretreatment with ammonia diffusion was required for ammonium prior to the persulfate oxidation. Up to 100 samples can be measured daily using the system. We can generally run 15N measurements with only 1-10 mL of sample for each chemical species of N, a volume 1/10-1/100 times smaller than the amount necessary for conventional methods. Our method is useful for measuring 15N with GC/MS, offering greater convenience than IRMS.
Nitrous oxide (N2O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH3 oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N2O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N2O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH3 oxidizers and denitrifiers, including the previously-overlooked taxa, in N2O emission from a cropland, and address the biological and environmental factors controlling the N2O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N2O production than the long-studied ones. We also demonstrated that the N2O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N2O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N2O production by overlooked denitrifying bacteria and N2O reduction by long-studied N2O-reducing bacteria after manure fertilization into the plowed layer; and (3) N2O production by NH3-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH3 oxidizers and denitrifiers, which will help us understand the environmental context-dependent N2O emission processes.
Soil microbial communities are intricately linked to ecosystem functioning such as nutrient cycling; therefore, a predictive understanding of how these communities respond to environmental changes is of great interest. Here, we test whether phylogenetic information can predict the response of bacterial taxa to nitrogen (N) addition. We analyze the composition of soil bacterial communities in 13 field experiments across 5 continents and find that the N response of bacteria is phylogenetically conserved at each location. Remarkably, the phylogenetic pattern of N responses is similar when merging data across locations. Thus, we can identify bacterial clades - the size of which are highly variable across the bacterial tree - that respond consistently to N addition across locations. Our findings suggest that a phylogenetic approach may be useful in predicting shifts in microbial community composition in the face of other environmental changes.
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