Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition

Organic matter decomposition and soil CO₂ efflux are both mediated by soil microorganisms, but the potential effects of temporal variations in microbial community composition are not considered in most analytical models of these two important processes. However, inconsistent relationships between rates of heterotrophic soil respiration and abiotic factors, including temperature and moisture, suggest that microbial community composition may be an important regulator of soil organic matter (SOM) decomposition and CO₂ efflux. We performed a short-term (12-h) laboratory incubation experiment using tropical rain forest soil amended with either water (as a control) or dissolved organic matter (DOM) leached from native plant litter, and analyzed the effects of the treatments on soil respiration and microbial community composition. The latter was determined by constructing clone libraries of small-subunit ribosomal RNA genes (SSU rRNA) extracted from the soil at the end of the incubation experiment. In contrast to the subtle effects of adding water alone, additions of DOM caused a rapid and large increase in soil CO₂ flux. DOM-stimulated CO₂ fluxes also coincided with profound shifts in the abundance of certain members of the soil microbial community. Our results suggest that natural DOM inputs may drive high rates of soil respiration by stimulating an opportunistic subset of the soil bacterial community, particularly members of the Gammaproteobacteria and Firmicutes groups. Our experiment indicates that variations in microbial community composition may influence SOM decomposition and soil respiration rates, and emphasizes the need for in situ studies of how natural variations in microbial community composition regulate soil biogeochemical processes.     

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four ¹³C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the ¹³C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-¹³C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by ¹³C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram + biomarkers showed more incorporation of SOM-C than did Gram – biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More ¹³C (from both simple and recalcitrant sources) was incorporated into the Gram – biomarkers than Gram + biomarkers despite the fact that the Gram + group generally comprised a greater portion of the bacterial biomass than did markers for the Gram – group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.     

Microbial community composition controls carbon flux across litter types in early phase of litter decomposition

Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non-labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition.     

Chemistry and Dynamics of Dissolved Organic Matter in a Temperate Coniferous Forest on Andic Soils: Effects of Litter Quality

Dissolved organic matter (DOM) plays an important role in transporting carbon and nitrogen from forest floor to mineral soils in temperate forest ecosystems. Thus, the retention of DOM via sorption or microbial assimilation is one of the critical steps for soil organic matter formation in mineral soils. The chemical properties of DOM are assumed to control these processes, yet we lack fundamental information that links litter quality, DOM chemistry, and DOM retention. Here, we studied whether differences in litter quality affect solution chemistry and whether changes in litter inputs affect DOM quality and removal in the field. The effects of litter quality on solution chemistry were evaluated using chemical fractionation methods for laboratory extracts and for soil water collected from a temperate coniferous forest where litter inputs had been altered. In a laboratory extraction, litter type (needle, wood, root) and the degree of decomposition strongly influenced solution chemistry. Root litter produced more than 10 times more water-extractable dissolved organic N (DON) than any other litter type, suggesting that root litter may be most responsible for DON production in this forest ecosystem. The chemical composition of the O-horizon leachate was similar under all field treatments (doubled needle, doubled wood, and normal litter inputs). O-horizon leachate most resembled laboratory extracts of well-decomposed litter (that is, a high proportion of hydrophobic acids), in spite of the significant amount of litter C added to the forest floor and a tendency toward higher mean DOM under doubled-Litter treatments. A lag in DOM production from added litter or microbial modification might have obscured chemical differences in DOM under the different treatments. Net DOM removal in this forest soil was strong; DOM concentration in the water deep in the mineral soil was always low regardless of concentrations in water that entered the mineral soil and of litter input manipulation. High net removal of DOM from O-horizon leachate, in spite of extremely low initial hydrophilic neutral content (labile DOM), coupled with the lack of influence by season or soil depth, suggests that DOM retention in the soil was mostly by abiotic sorption.     

Links between plant community composition,soil organic matter quality and microbial communities in contrasting tundra habitats

Plant communities, soil organic matter and microbial communities are predicted to be interlinked and to exhibit concordant patterns along major environmental gradients. We investigated the relationships between plant functional type composition, soil organic matter quality and decomposer community composition, and how these are related to major environmental variation in non-acid and acid soils derived from calcareous versus siliceous bedrocks, respectively. We analysed vegetation, organic matter and microbial community compositions from five non-acidic and five acidic heath sites in alpine tundra in northern Europe. Sequential organic matter fractionation was used to characterize organic matter quality and phospholipid fatty acid analysis to detect major variation in decomposer communities. Non-acidic and acidic heaths differed substantially in vegetation composition, and these disparities were associated with congruent shifts in soil organic matter and microbial communities. A high proportion of forbs in the vegetation was positively associated with low C:N and high soluble N:phenolics ratios in soil organic matter, and a high proportion of bacteria in the microbial community. On the contrary, dwarf shrub-rich vegetation was associated with high C:N and low soluble N:phenolics ratios, and a high proportion of fungi in the microbial community. Our study demonstrates a strong link between the plant community composition, soil organic matter quality, and microbial community composition, and that differences in one compartment are paralleled by changes in others. Variation in the forb-shrub gradient of vegetation may largely dictate variations in the chemical quality of organic matter and decomposer communities in tundra ecosystems. Soil pH, through its direct and indirect effects on plant and microbial communities, seems to function as an ultimate environmental driver that gives rise to and amplifies the interactions between above- and belowground systems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria

Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.     

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land‐cover change affects belowground carbon storage and nutrient availability. We measured intra‐ and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well‐replicated, long‐term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter‐ and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land‐use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities.     

Plant Communities, Soil Microorganisms, and Soil Carbon Cycling: Does Altering the World Belowground Matter to Ecosystem Functioning?

Soil microorganisms mediate many critical ecosystem processes. Little is known, however, about the factors that determine soil microbial community composition, and whether microbial community composition influences process rates. Here, we investigated whether aboveground plant diversity affects soil microbial community composition, and whether differences in microbial communities in turn affect ecosystem process rates. Using an experimental system at La Selva Biological Station, Costa Rica, we found that plant diversity (plots contained 1, 3, 5, or > 25 plant species) had a significant effect on microbial community composition (as determined by phospholipid fatty acid analysis). The different microbial communities had significantly different respiration responses to 24 labile carbon compounds. We then tested whether these differences in microbial composition and catabolic capabilities were indicative of the ability of distinct microbial communities to decompose different types of litter in a fully factorial laboratory litter transplant experiment. Both microbial biomass and microbial community composition appeared to play a role in litter decomposition rates. Our work suggests, however, that the more important mechanism through which changes in plant diversity affect soil microbial communities and their carbon cycling activities may be through alterations in their abundance rather than their community composition.     

Experimental litterfall manipulation drives large and rapid changes in soil carbon cycling in a wet tropical forest

Global changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and storage remain largely unknown, especially in C‐rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2 years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO ₂ fluxes; the relative decline in CO ₂ production was greater in the litter removal plots (?22%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO ₂ fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.     

Effects of grassland species on decomposition of litter and soil microbial communities

Decomposition of litter is greatly influenced not only by its chemical composition but also by activities of soil decomposers. By using leaf litter from 15 plant species collected from semi-natural and improved grasslands, we examined (1) how interspecific differences in the chemical composition of litter influence the abundance and composition of soil bacterial and fungal communities and (2) how such changes in microbial communities are related to the processes of decomposition. The litter from each species was incubated in soil of a standard composition for 60 days under controlled conditions. After incubation, the structure of bacterial and fungal communities in the soil was examined using phospholipid fatty-acid analysis and denaturing gradient gel electrophoresis. Species from improved grasslands had significantly higher rates of nitrogen mineralization and decomposition than those from semi-natural grasslands because the former were richer in nitrogen. Litter from improved grasslands was also richer in Gram-positive bacteria, whereas that from semi-natural grasslands was richer in actinomycetes and fungi. Nitrogen content of litter also influenced the composition of the fungal community. Changes in the composition of both bacterial and fungal communities were closely related to the rate of litter decomposition. These results suggest that plant species greatly influence litter decomposition not only through influencing the quality of substrate but also through changing the composition of soil microbial communities.     

Tropical tree species composition affects the oxidation of dissolved organic matter from litter

Plant species effects on soil nutrient availability are relatively well documented, but the effects of species differences in litter chemistry on soil carbon cycling are less well understood, especially in the species-rich tropics. In many wet tropical forest ecosystems, leaching of dissolved organic matter (DOM) from the litter layer accounts for a significant proportion of litter mass loss during decomposition. Here we investigated how tree species differences in soluble dissolved organic C (DOC) and nutrients affected soil CO₂ fluxes in laboratory incubations. We leached DOM from freshly fallen litter of six canopy tree species collected from a tropical rain forest in Costa Rica and measured C-mineralization. We found significant differences in litter solubility and nutrient availability. Following DOM additions to soil, rates of heterotrophic respiration varied by as much as an order of magnitude between species, and overall differences in total soil CO₂ efflux varied by more than four-fold. Variation in the carbon: phosphorus ratio accounted for 51% of the variation in total CO₂ flux between species. These results suggest that tropical tree species composition may influence soil C storage and mineralization via inter-specific variation in plant litter chemistry.     

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO₂ concentrations or atmospheric nutrient deposition.     

Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

Background and aims

Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore, the effect of a litter species in the biogeochemical cycle of its current environment may not predict patterns after migration. Under a tree migration sequence we test whether litter quality alone drives litter decomposition, or whether soil communities modify quality effects.

Methods

Litter and soils were sampled across an elevation gradient of different overstory species where lower elevation species are predicted to migrate upslope. We use a common garden, laboratory microcosm design (soil community x litter environment) with single and mixed-species litters.

Results

We find significant litter quality and microbial community effects (P?<?0.001), explaining 47 % of the variation in decomposition for mixed-litters.

Conclusion

Soil community effects are driven by the functional breadth, or historical exposure, of the microbial communities, resulting in lower decomposition of litters inoculated with upslope communities. The litter x soil community interaction suggests that litter decomposition rates in forests of changing tree species composition will be a product of both litter quality and the recipient soil community.     

Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter

Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.     

贺兰山不同林分凋落物微生物群落特征与影响因素

贺兰山是我国重要生态屏障,贺兰山生态森林生态系统保护受到极大关注,森林凋落物及土壤微生物对全球气候变化研究具有重要意义。目前,贺兰山不同林分的凋落物分解过程中微生物群落结构特征差异、不同凋落物化学组成对微生物群落结构的影响尚不清楚。以贺兰山具有代表性的3种林分（油松林、青海云杉林以及油松-山杨混交林）凋落物为研究对象,开展凋落物化学组成、微生物群落组成及多样性特征研究,揭示不同林分凋落物的优势微生物群落特征和影响因子。结果表明,3种林分凋落物的细菌和真菌在多个多样性指数之间差异性均不显著,但是在多样性指数中真菌PD whole tree指数显著大于细菌,真菌Shannon指数与Ghao1指数却显著小于细菌。在门水平上不同林分凋落物的微生物优势菌类无显著差异,但在属水平上差异显著,而且细菌差异小于真菌,在各个分类水平上,凋落物细菌和真菌群落组成均表现为油松-山杨混交林＜青海云杉林＜青海云杉林,凋落物微生物多样性在青海云杉林中最为丰富。细菌不同节点间连接线负相关数量略大于正相关,真菌则相反。油松林凋落物与其它林分凋落物相比,微生物群落之间联系更加紧密。油松林凋落物OC含量最大、青海云杉林凋落物的TK含量最大、油松-山杨混交林的TN含量最大,且在3种林分中显著差异。相关性分析表明OC、TN、TP、TK是影响凋落物细菌和真菌群落组成及多样性的主要因素,冗余分析表明不同林分凋落物的微生物多样性指数受养分影响,凋落物OC、TN、TP、TK是影响微生物群落组成和多样性的重要因素,其中OC与微生物群落多样性相关性最显著,是影响凋落物细菌和真菌群落组成和多样性最主要的因子。     

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (?31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin‐derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin‐derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin‐derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.     

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot efficiently utilize tDOM and that in subarctic estuaries other factors are responsible for the removal of imported tDOM.     

Soil Water Content and Organic Carbon Availability Are Major Determinants of Soil Microbial Community Composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (–C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.     

Composition,Dynamics, and Fate of Leached Dissolved Organic Matter in Terrestrial Ecosystems: Results from a Decomposition Experiment

Fluxes of dissolved organic matter (DOM) are an important vector for the movement of carbon (C) and nutrients both within and between ecosystems. However, although DOM fluxes from throughfall and through litterfall can be large, little is known about the fate of DOM leached from plant canopies, or from the litter layer into the soil horizon. In this study, our objectives were to determine the importance of plant-litter leachate as a vehicle for DOM movement, and to track DOM decomposition [including dissolve organic carbon (DOC) and dissolved organic nitrogen (DON) fractions], as well as DOM chemical and isotopic dynamics, during a long-term laboratory incubation experiment using fresh leaves and litter from several ecosystem types. The water-extractable fraction of organic C was high for all five plant species, as was the biodegradable fraction; in most cases, more than 70% of the initial DOM was decomposed in the first 10 days of the experiment. The chemical composition of the DOM changed as decomposition proceeded, with humic (hydrophobic) fractions becoming relatively more abundant than nonhumic (hydrophilic) fractions over time. However, in spite of proportional changes in humic and nonhumic fractions over time, our data suggest that both fractions are readily decomposed in the absence of physicochemical reactions with soil surfaces. Our data also showed no changes in the ¹³C signature of DOM during decomposition, suggesting that isotopic fractionation during DOM uptake is not a significant process. These results suggest that soil microorganisms preferentially decompose more labile organic molecules in the DOM pool, which also tend to be isotopically heavier than more recalcitrant DOM fractions. We believe that the interaction between DOM decomposition dynamics and soil sorption processes contribute to the ¹³C enrichment of soil organic matter commonly observed with depth in soil profiles. published online 2004     

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.