Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon (original) (raw)
Frontiers in Microbiology, 2018
Mineral nitrogen (N) availability to heterotrophic microorganisms is known to impact organic matter (OM) decomposition. Different pathways determining the N accessibility depend to a large extent on soil structure. Contact between soil mineral and OM substrate particles can facilitate N transport toward decomposition hot spots. However, the impact of soil structure on N availability to microbes and thus heterotrophic microbial activity and community structure is not yet fully understood. We hypothesized that carbon mineralization (Cmin) from low-N substrate would be stimulated by increased N availability caused by closer contact with soil particles or by a higher moisture level, enhancing potential for N-diffusion. Under opposite conditions retarded heterotrophic activity and a dominance of fungi were expected. A 128-days incubation experiment with CO 2 emission monitoring from artificially reconstructed miniature soil cores with contrasting soil structures, viz. high or low degree of contact between soil particles, was conducted to study impacts on heterotrophic activity. The soil cores were subjected to different water filled pore space percentages (25 or 50% WFPS) and amended with either easily degradable OM high in N (grass) or more resistant OM low in N (sawdust). X-ray µCT image processing allowed to quantify the pore space in 350 µm around OM substrates, i.e., the microbial habitat of involved decomposers. A lower local porosity surrounding sawdust particles in soils with stonger contact was confirmed, at least at 25% WFPS. Mineral N addition to sawdust amended soils with small particle contact at 25% WFPS resulted in a stimulated respiration. Cmin in the latter soils was lower than in case of high particle contact. This was not observed for grass substrate particles or at 50% WFPS. The interactive effect of substrate type and soil structure suggests that the latter controls Cmin through mediation of N diffusion and in turn N availability. Phospholipid fatty acid did not reveal promotion of fungal over bacterial biomarkers in treatments with N-limited substrate decomposition. Combining X-ray µCT with tailoring soil structure allows for more reliable investigation of effects on the soil microbial community, because as also found here, the established soil pore network structure can strongly deviate from the intended one.
Applied and Environmental Microbiology, 2002
Stable C and N isotopes have long been used to examine properties of various C and N cycling processes in soils. Unfortunately, relatively large sample sizes are needed for accurate gas phase isotope ratio mass spectrometric analysis. This limitation has prevented researchers from addressing C and N cycling issues on microbially meaningful scales. Here we explored the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) to detect 13 C and 15 N assimilation by individual bacterial cells and to quantify N isotope ratios in bacterial samples and individual fungal hyphae. This was accomplished by measuring the relative abundances of mass 26 ( 12 C 14 N ؊ ) and mass 27 ( 13 C 14 N ؊ and 12 C 15 N ؊ ) ions sputtered with a Ga ؉ probe from cells adhered to an Si contact slide. TOF-SIMS was successfully used to locate and quantify the relative 15 N contents of individual hyphae that grew onto Si contact slides in intimate contact with a model organomineral porous matrix composed of kaolin, straw fragments, and freshly deposited manure that was supplemented with 15 NO 3 ؊ . We observed that the 15 N content of fungal hyphae grown on the slides was significantly lower in regions where the hyphae were influenced by N-rich manure than in regions influenced by N-deficient straw. This effect occurred over distances of tens to hundreds of microns. Our data illustrate that TOF-SIMS has the potential to locate N-assimilating microorganisms in soil and to quantify the 15 N content of cells that have assimilated 15 N-labeled mineral N and shows promise as a tool with which to explore the factors controlling microsite heterogeneities in soil.
Reviews and syntheses: Iron: A driver of nitrogen bioavailability in soils?
An adequate supply of bioavailable nitrogen (N) is critical to soil microbial communities and plants. Over the last decades, research efforts have rarely considered the importance of reactive iron (Fe) minerals in the processes that produce or consume bioavailable N in soils, compared to other factors such as soil texture, pH, and organic matter (OM). However, Fe is involved in both enzymatic and non-enzymatic reactions that influence the N cycle. More broadly, reactive Fe minerals restrict soil organic matter (SOM) cycling through sorption processes, but also promote SOM decomposition and denitrification in anoxic conditions. By synthesizing available research, we show that Fe plays diverse roles in N bioavailability. Fe affects N bioavailability directly by acting as a sorbent, catalyst, and electron transfer agent, or indirectly by promoting certain soil features, such as aggregate formation and stability, which affect N turnover processes. These roles can lead to different outcomes on N bioavailability, depending on environmental conditions such as soil redox shifts during wet-dry cycles. We provide examples of Fe-N interactions and discuss the possible underlying mechanisms, which can be abiotic or microbially meditated. We also discuss methodological constraints that hinder the development of mechanistic understanding of Fe in controlling N bioavailability and highlight the areas of needed research. 1 Introduction Terrestrial ecosystem productivity is largely constrained by nitrogen (N) availability (Vitousek and Howarth, 1991). The largest pool of N in these ecosystems is found in soils which contains 133-140 Pg of total N globally within the first top 100 cm of soil (Batjes, 1996). A clear description of the factors controlling N bioavailability in soils is needed to design agricultural practices that meet crop demand and mitigate N loss to the environment. A large literature exists on the effects of soil texture, OM, mineral N inputs, pH, moisture, and microbial communities on N mineralization. However, geochemical factors, such as reactive Fe minerals, are rarely considered in N cycling, though they are often studied as vital components of carbon (C) cycling. Since C and N cycles are interconnected in soils (Feng et al., 2019; Gärdenäs et al., 2011), they should be regulated
Biogeochemistry, 2009
Sequential density fractionation separated soil particles into “light” predominantly mineral-free organic matter vs. increasingly “heavy” organo-mineral particles in four soils of widely differing mineralogy. With increasing particle density C concentration decreased, implying that the soil organic matter (OM) accumulations were thinner. With thinner accumulations we saw evidence for both an increase in 14C-based mean residence time (MRT) of the OM and a shift from plant to microbial origin.Evidence for the latter included: (1) a decrease in C/N, (2) a decrease in lignin phenols and an increase in their oxidation state, and (3) an increase in δ13C and δ15N. Although bulk-soil OM levels varied substantially across the four soils, trends in OM composition and MRT across the density fractions were similar. In the intermediate density fractions (~1.8–2.6 g cm−3), most of the reactive sites available for interaction with organic molecules were provided by aluminosilicate clays, and OM characteristics were consistent with a layered mode of OM accumulation. With increasing density (lower OM loading) within this range, OM showed evidence of an increasingly microbial origin. We hypothesize that this microbially derived OM was young at the time of attachment to the mineral surfaces but that it persisted due to both binding with mineral surfaces and protection beneath layers of younger, less microbially processed C. As a result of these processes, the OM increased in MRT, oxidation state, and degree of microbial processing in the sequentially denser intermediate fractions. Thus mineral surface chemistry is assumed to play little role in determining OM composition in these intermediate fractions. As the separation density was increased beyond ~2.6 g cm−3, mineralogy shifted markedly: aluminosilicate clays gave way first to light primary minerals including quartz, then at even higher densities to various Fe-bearing primary minerals. Correspondingly, we observed a marked drop in δ15N, a weaker decrease in extent of microbial processing of lignin phenols, and some evidence of a rise in C/N ratio. At the same time, however, 14C-based MRT time continued its increase. The increase in MRT, despite decreases in degree of microbial alteration, suggests that mineral surface composition (especially Fe concentration) plays a strong role in determining OM composition across these two densest fractions.
The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent
Environmental Science and Pollution Research, 2013
Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.
Biogeochemistry
Despite decades of research progress, ecologists are still debating which pools and fluxes provide nitrogen (N) to plants and soil microbes across different ecosystems. Depolymerization of soil organic N is recognized as the rate-limiting step in the production of bioavailable N, and it is generally assumed that detrital N is the main source. However, in many mineral soils, detrital polymers constitute a minor fraction of total soil organic N. The majority of organic N is associated with clay-sized particles where physicochemical interactions may limit the accessibility of N-containing compounds. Although mineralassociated organic matter (MAOM) has historically been considered a critical, but relatively passive, reservoir of soil N, a growing body of research now points to the dynamic nature of mineral-organic associations and their potential for destabilization. Here we synthesize evidence from biogeoscience and soil ecology to demonstrate how MAOM is an important, yet overlooked, mediator of bioavailable N, especially in the rhizosphere. We highlight several biochemical strategies that enable plants and microbes
Relation between carbon and nitrogen turnover in soil organic fractions of microbial origin
Soil Biology and Biochemistry, 1975
Labelled 14C-acetate and "N-(NH&SO, were added to a clay soil in the laboratory to follow transformations of microbial C and N. A fungal population developed initially. reaching a maximum by day 5, then rapidly declined and was replaced by a population dominated by bacteria and actinomycetes. Soil samples containing doubly-labelled microorganisms and their metabolites were extracted by Na,P,O,, and the extracted material further separated with phenol. The highly labelled acid-soluble (fulvic acid) fraction of the Na,P20, extract contained extracellular metabolites of low molecular weight which were rapidly attacked and converted to new microbial biomass, metabolites, mineral N or COZ. Na4PZ0, also removed an acid-insoluble (humic acid) fraction of which up to 70 per cent of the labelled C and N could be removed by phenol. Attack of these recently synthesized extracellular materials was indicated by a rapid decline of Na,P20, extractable C and N during the growth of bacteria and actinomycetes. Following Na,P,O, extraction, the residue was sonicated and peptized in water and the components of the microbial biomass were partitioned into sedimentation fractions by centrifugation. The components concentrated in the >0,2 pm fraction, which were hypothesized as being cell wall components, were more resistant to attack than materials in the (0.04 pm fraction. The materials in the latter fraction were thought to originate from cytoplasmic constituents. The labeiled materials in the co.04 pm sized fraction, which accumulated as the fungal population developed, were utilized less rapidly by the developing bacterial population. Decomposition of the microbial population resulted in transfer of C and N through various sediment fractions. The organic fraction (considered to be cytoplasmic material and adsorbed extracellular metabolites) which became labelled as the bacterial population developed, was utilized less rapidly by the developing bacterial population than components removable by Na,P20,. Evolution of "C02. production of microbial material and immobilization of N closely paralleled the incorporation and release of these elements from the fractions. The similarity of the behavior patterns of these elements suggested they were intimately associated within the soil microbial system studied. This demonstrated that N transformations were highly dependent on C transformations.