Litter Microbial Community Research Articles

Predominant effects of litter chemistry on lignin degradation in the early stage of leaf litter decomposition

Lignin has long been considered a recalcitrant component of plant materials. Its degradation is critical for litter decomposition and the formation of soil organic matter. However, little is known about lignin degradation dynamics and its controlling factors during leaf litter decomposition, especially in forest ecosystems. The objective of this study was to evaluate lignin degradation dynamics during litter decomposition and its controlling factors. We conducted a lab incubation experiment for 180 days with leaves of two tree species (Fagus lucida and Schima parviflora) from a mid-subtropical forest in China. The CuO oxidation method was applied for lignin determination. The mass loss of bulk litter and lignin (including V-, S- and C-type phenols) and the dynamics of litter microbial community composition, carbon, nitrogen (N) and phosphorus (P) were determined during the incubation. Lignin degradation appeared to be a two-phase process over the incubation period, including a fast decomposition phase (early stage) followed by a relatively slow decomposition phase (late stage). Additionally, 21.9% and 18.5% of the initial lignin contents were lost from F. lucida and S. parviflora litter, respectively. The acid to aldehyde ratios of V-type phenols [(Ac/Al)V] and S-type phenols [(Ac/Al)S] of both litters increased with incubation. Lignin degradation was significantly affected by the litter types but not by the soil microbial communities, given that the soil microbial communities were distinctly different for the two plant communities. In the early stage, the mass loss of lignin from the F. lucida litter was faster than the S. parviflora litter: the mass loss of S-type phenols from the F. lucida litter was faster than the S. parviflora litter, whereas the dynamics of the V-type phenols were comparable for the two species. For F. lucida litter, lignin was lost faster than the bulk litter in the early stage but no difference was observed after day 133. For S. parviflora litter, the degradation of lignin and bulk litter were generally comparable over the incubation period. The mass loss of lignin in the early stage was significantly correlated with lignin, N and P contents, and the carbon/N, carbon/P and N/P ratios. Among these factors, P played a prominent role in controlling lignin degradation. The important role of litter chemistry emphasized the importance of taking this into account in plant-soil models assessing carbon dynamics in forest ecosystems. These results improve our conceptual understanding of lignin degradation and its controlling factors.

Stoichiometric plasticity of microbial communities is similar between litter and soil in a tropical rainforest

Heterotrophic microorganisms are commonly thought to be stoichiometrically homeostatic but their stoichiometric plasticity has rarely been examined, particularly in terrestrial ecosystems. Using a fertilization experiment in a tropical rainforest, we evaluated how variable substrate stoichiometry may influence the stoichiometry of microbial communities in the leaf litter layer and in the underlying soil. C:N:P ratios of the microbial biomass were higher in the organic litter layer than in the underlying mineral soil. Regardless of higher ratios for litter microbial communities, C, N, and P fertilization effects on microbial stoichiometry were strong in both litter and soil, without any fundamental difference in plasticity between these two communities. Overall, N:P ratios were more constrained than C:nutrient ratios for both litter and soil microbial communities, suggesting that stoichiometric plasticity arises because of a decoupling between C and nutrients. Contrary to the simplifying premise of strict homeostasis in microbial decomposers, we conclude that both litter and soil communities can adapt their C:N:P stoichiometry in response to the stoichiometric imbalance of available resources.

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semi‐arid woodland in Patagonia, Argentina

SummaryLarge‐scale disturbances can be important components of the temporal landscape of natural ecosystems, but generalities regarding ecosystem impacts are difficult due to their infrequent and unpredictable nature. Volcanic eruptions figure as one of the most prominent of these natural disturbances, but the effects on microbes and ground‐dwelling arthropods, which modulate carbon and nutrient turnover, are relatively unknown.We evaluated the effects of the 2011 Puyehue‐Cordón Caulle eruption in Patagonia, Argentina, on the litter and soil microbial and faunal communities in natural and afforested semi‐arid ecosystems located 70 km west of the epicentre of the eruption. We hypothesized that volcanic ash deposition would strongly reduce soil faunal and microbial communities due to insecticidal effects of ash on arthropods, with a concomitant reduction in ecosystem processes.Our objective was to quantify the impact of the volcanic eruption by comparing pre‐ and post‐eruption time points in the same study site, with nearly identical field methodology. We measured environmental variables of soil and litter moisture, pH, microbial biomass, and soil and litter microbial enzymatic activity. We evaluated ground‐dwelling arthropods and nematodes using pitfall traps and soil extraction, respectively. Additionally, a parallel, controlled‐condition experiment of simulated ash deposition was conducted to evaluate ash effects on litter decomposition and enzymatic activity.In the field, post‐eruption soils had lower soil water content, pH and soil organic matter. Additionally, nematode abundance and soil microbial enzyme activity were significantly reduced. In contrast, ground‐dwelling arthropods and litter enzymatic activity increased significantly. Finally, with simulated ash deposition, litter decomposition increased fourfold for native litter decomposition.Large‐scale disturbances may play a key role in biogeochemical cycling in affected natural ecosystems, but not necessarily due to their catastrophic effects. In contrast to our original predictions, we observed a marked stimulation of biotic activity and carbon turnover in the aftermath of the Puyehue volcanic eruption, which demonstrates that the biotic component of these ecosystems has a substantial capacity to respond to these disturbances in short time frames. These results can contribute to placing the role of these large‐scale infrequent disturbances in a more robust ecological context.ALay Summaryis available for this article.

Is there a convergence of deciduous leaf litter stoichiometry, biochemistry and microbial population during decay?

Litter decomposition is driven by saprotrophic microbial communities. The structure of this community varies over the course of decomposition, which has been linked to the chemistry of litter resources. Here, we test the hypothesis that leaf litter from different tree species becomes more similar in terms of litter stoichiometry, C-biochemistry during the course of decomposition (convergence).We also test if these variations can be linked to shifts in microbial community structure and abundance. For this reason, leaf litter of four deciduous tree species — beech (Fagus sylvatica), oak (Quercus robur), alder (Alnus glutinosa) and ash (Fraxinus excelsior) were sampled from a temperate forest in February, May and September 2010. We measured variations in leaf litter stoichiometry by elemental concentrations, C-biochemistry with Fourier transform infrared (FTIR) spectroscopy and litter microbial community structure and abundance with phospholipid fatty acid (PLFA) analysis. For litter from beech, oak and ash, C:N and C:P ratio converged with time when exposed to the same environmental conditions during degradation. In contrast, C:nutrient ratios increased in alder litter over time. Litter C-biochemistry was to a large extent related to shifts in C:N ratios. Principal component analysis PCA of FTIR bands, revealed that divergence in C-biochemistry over the course of decomposition was dependent on litter type, and hence, with initial C:N ratio. Litter-decomposing bacterial community was highly relevant to C-biochemistry and environmental conditions (temperature and moisture) while fungi community was more nutrients-related.In conclusion, initially wide C:nutrient ratios tend to converge during decay; while nutrient limitation may lead to divergence of stoichiometry. In general, there was a trend towards divergence of C-biochemistry and microbial community structure.

Distance from the sea as a driving force of microbial communities under water potential stresses in litters of two typical Mediterranean plant species

Though many studies have focused on the incidence of drought, little attention has been paid to osmotic stress and to how the interaction of the two stresses impacts microbial functioning. Moreover, deciphering how certain environmental factors such as distance from the sea or type of litter may shape microbial responses to these stresses is of huge importance. The objective of this study is to shed light on the impact of matric and osmotic stresses (combined or not) on litter microbial communities potentially shaped differently by either plant species or distance from the sea. Two Mediterranean plant species, Cistus albidus L. and Pistacia lentiscus L., collected from both inland and coastal areas, were used to set up a total of 72 mesocosms (4 mesocosms×3 types of litters (pure or mixed)×2 sites (coastal and inland)×3 types of stress). A first set of twenty four mesocosms ‘control’ (4 mesocosms×3 types of litters (pure or mixed)×2 sites (coastal and inland)) were maintained under favourable conditions for 60days (25°C, 600g·kg−1 water content). For matric stress, twenty four mesocosms were subjected to 5 drying/rewetting cycles (7days at 25°C/7days at 600g·kg−1 water content and 25°C). For osmotic stress, twenty four mesocosms received 10mg of chlorine ions per g of litter using NaCl and then were incubated at 600g·kg−1 water content and 25°C for 60days. The last twenty four mesocosms were subjected to the combined drought and salt stresses for 60days. Resistance to added osmotic stress was also tested. Catabolic diversity assessed via Biolog Ecoplates, was higher in coastal than in inland areas after drought and combined stresses. Moreover, catabolic profiles were shaped differently after stresses depending on the litter type. Basal respiration withstood an added severe drought stress better in microbial communities previously subjected to combined stresses. Resistance to an added osmotic stress was higher in inland litters previously subjected to salt stress. Microbial communities from the coastal area were more able to maintain their catabolic potential and thus to withstand these stresses. Combined stresses and osmotic stress reinforced resistance to added severe drought or osmotic stress respectively. Thus our findings reveal that microbial communities previously subjected to water potential stresses were more capable to overcome additional stresses of similar nature, suggesting adaptation mechanisms to such type of stresses.

Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study

Litter decomposition is a key process for ecosystem fertility and carbon (C) balance, key uncertainties remain about how this fundamental process is affected by microbial community composition. Evidence is growing that plant litter generally decays fastest at the site from which it was derived, owing to the presence of specialized microbial communities that can decompose specific types of litter. The objectives were to determine the impact of sites on litter decomposition and to examine the relationships among microbial community composition, litter chemistry, and decomposition rates of coniferous Cunninghamia lanceolata litter of higher lignin content and broadleaved Mytilaria laosensis litter of lower lignin content at different stages of decomposition under plantations of the respective species. The study was conducted for 16 months using a randomized split-plot design experiment with four replications of all combinations of treatments, the treatments being litter type and site (plantation species). The results showed that decomposition rates were the same for all combinations of amendments and sites, meaning that both sites had microbial communities equally capable or adapted to decompose plant substrates it had not previously encountered, despite marked differences in soil microbial communities between sites and the chemistry of the two litter types. Initial M. laosensis litter was of lower lignin content and C:N ratio and decomposed faster in the first 8 months than C. lanceolata litter under either M. laosensis or C. lanceolata forest. Litter decomposition was significantly slower in the environment from which it was derived between month 8 and month 16. This could be attributed to the exceptionally poor decomposition of M. laosensis litter which was significantly higher lingnin content at month 8 under M. laosensis than under C. lanceolata due to the impact of site on preferential degradation of litter C. Decomposers under C. lanceolata forest were more efficient in degrading alkyl C and/or less efficient in degrading O-alkyl C than those under M. laosensis forest during the experimental period, which might be related to the microbial community composition in the decomposing litter. Our study clearly showed interactions between changing litter chemistry and litter microbial communities and their impacts on litter decomposition. Site was not important in impacting decomposition rates, but played an important role in the preferential degradation of C components. However, further studies are needed to examine the conditions in forests where more rapid litter decomposition beneath the parent species than another species is considered to be common, in order to improve our ability to model decomposition globally.

Disease suppression in winter wheat from novel symbiosis with forest fungi

Abstract In the Pacific Northwest, USA, pathogenic Fusarium spp. are common in agricultural soils but rare in forest soils. We hypothesized that regional forest soils possess indigenous Fusarium- suppressive microbes, which may enter into novel associations with introduced crop plants, potentially contributing to suppressive soils. To test this hypothesis, we inoculated winter wheat with regional forest litter microbial communities and rhizosphere fungi and challenged plants with pathogenic Fusarium culmorum from regional agricultural fields. We also challenged plants with drought and low-temperature stress, which may augment disease severity. A forest litter microbiome improved survival of Fusarium -infected wheat three-fold and increased growth by 67%. Seedlings inoculated with individual forest fungi developed larger root systems during vernalization. Penicillium sp. doubled yield of Fusarium -infected winter wheat exposed to drought conditions. Indigenous microbes from native plant communities of the interior Northwest mitigate abiotic stresses and may contribute to suppression of a soil-borne wheat disease via novel symbioses.

Nitrogen Cycling Potential of a Grassland Litter Microbial Community.

Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems.

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.

Temporal variation overshadows the response of leaf litter microbial communities to simulated global change

Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the response of the bacterial and fungal communities to the treatments and compare these results to background, temporal (seasonal and interannual) variability of the communities. We found that the drought and nitrogen treatments both had significant effects on microbial community composition, explaining 2-6% of total compositional variation. However, microbial composition was even more strongly influenced by seasonal and annual variation (explaining 14-39%). The response of microbial composition to drought varied by season, while the effect of the nitrogen addition treatment was constant through time. These compositional responses were similar in magnitude to those seen in microbial enzyme activities and the surrounding plant community, but did not correspond to a consistent effect on leaf litter decomposition rate. Overall, these patterns indicate that, in this ecosystem, temporal variability in the composition of leaf litter microorganisms largely surpasses that expected in a short-term global change experiment. Thus, as for plant communities, future microbial communities will likely be determined by the interplay between rapid, local background variability and slower, global changes.

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities

Focusing on Sumatra, a hotspot of tropical lowland rainforest transformation, we investigated effects of the con- version of rainforests into rubber agroforests (Bjungle rubber^), intensive rubber, and oil palm plantations on the communities of litter and soil microorganisms and identified factors responsible for these changes. Litter basal respiration, microbial biomass, total bacterial phospholipid fatty acids (PLFAs), and fungal PLFAs did not vary significantly with rainforest conversion. In litter of converted ecosystems, the concentration of certain PLFAs including the Gram-negative bacteria marker PLFA cy17:0 and the Gram-positive bacteria marker PLFA i17:0 was reduced as compared to rainforest, whereas the concentration of the arbuscular mycorrhizal fungi (AMF) marker neutral lipid fatty acid (NLFA) 16:1ω5c in- creased. As indicated by redundancy analysis, litter pH and carbon concentration explained most of the variation in litter microbial community composition. In soil, microbial biomass did not vary significantly with rainforest conversion, whereas basal respiration declined. Total PLFAs and especially that of Gram-negative bacteria decreased, whereas PLFA i17:0 in- creased with rainforest conversion. The concentration of fun- gal PLFAs increased with rainforest conversion, whereas NLFA 16:1ω5c did not change significantly. Redundancy analysis indicated that soil pH explained most of the variation in soil microbial community composition. Overall, the data suggest that conversion of rainforests into production systems results in more pronounced changes in microbial community composition in soil as compared to litter. In particular, the response of fungi and bacteria was more pronounced in soil, while the response of AMF was more pronounced in litter. Notably, only certain bacterial markers but not those of saprotrophic fungi and AMF were detrimentally affected by rainforest conversion.

Effects of a simulated hurricane disturbance on forest floor microbial communities

Forest floor microbial communities play a critical role in the processes of decomposition and nutrient cycling. The impact of cultivation, contamination, fire, and land management on soil microbial communities have been studied but there are few studies of microbial responses to the effects of tropical storms. The Canopy Trimming Experiment was executed in the Luquillo Experimental Forest of Puerto Rico to decouple two prominent effects of a hurricane—canopy opening and debris deposition on the forest floor—on forest biota and processes. We studied the independent and interactive hurricane effects of canopy openness and debris deposition on the relative abundance and diversity of microorganisms in soil and leaf litter using ester link fatty acids methyl esters (EL-FAME) analysis, and terminal restriction fragment length polymorphism (TRFLP) profile. Non-metric multi-dimensional scaling analysis of soil FAME showed soil microbial community composition was significantly different between pre- and post-hurricane periods including in the unmanipulated plots and among blocks, but there was no significant separation among treatments. This shows that there are strong spatiotemporal dynamics in the structure of soil microbial communities which masked hurricane effects (canopy opening and deposition of green debris). The degree of difference among treatments decreased with time in soil which suggests that our study may have started too late after the manipulations and therefore missed the effects of canopy opening and debris addition. This reflects the resilience of the soil microbial communities. The richness of soil bacterial TRF’s however, showed a significant positive response to added debris. Neither fungal nor bacterial NMDS clusters for leaf microbial communities showed significant grouping by treatment, time or litter cohorts. Significant differences were observed through time for fungal diversity in green leaves and for both bacterial and fungal diversity in senesced leaves. Senesced leaves microbial succession apparently stopped when both the canopy and debris were removed, and there was a suggestive trimming by time interaction which reflects the susceptibility of the leaf litter microbial community. Our findings contribute to the understanding of how microbial community structures can be affected by hurricane disturbances and forestry management practices that remove canopy and debris from the forest floor, and shows the need to analyze the microbial community immediately after the disturbance. Short-term changes in microbial communities due to forest disturbances can have significant implications for litter decomposition, soil organic matter accumulation, nutrient cycling, and food web dynamics in tropical forests. All of these factors should be taken into consideration when selecting the appropriate forest management practice.

Warming alters potential enzyme activity but precipitation regulates chemical transformations in grass litter exposed to simulated climatic changes

Warming generally accelerates the decomposition of plant litter. However, changes in precipitation could alter the sensitivity of litter decomposition to warming, thereby affecting the formation of litter-derived soil organic matter. As grassland soils store ∼20% of Earth's soil carbon, understanding the effect of climatic changes on the decomposition dynamics of grasses is important. However, little is known about how projected changes in climate would affect litter microbial communities and enzyme activities, and the consequences of these changes for the mass loss and compound-specific degradation of grass litter that possess complex lignocellulosic chemistry. Over a period of two years, using litter of the grass Poa trivialis, we studied how mass loss, microbial enzyme activity and fine-level litter chemistry responded to a factorial combination of 4 levels of warming (up to ambient +∼4 °C) and three levels of precipitation [ambient, wet (+50%) and dry (−50%)] at the Boston-Area Climate Experiment (BACE), in Massachusetts, USA. After 393 days of decomposition, supplemental precipitation accelerated mass loss compared to the dry treatment, as a consequence of faster loss of hydroxycinnamates, which protect carbohydrates through cross-linkages with lignins. Only a third as much of the cell wall-bound ferulic and p-coumaric acids remained in litter from the supplemental precipitation treatment compared to the ambient controls. In contrast, the warming treatments did not affect mass loss until later, after 740 days, when the litter in the warmest treatment (+∼4 °C) had lost the most mass. Although warming significantly affected mass loss after 740 days, there was also a trend in the warmest treatments toward greater mass loss in the wet (78% mass loss) and ambient (68%) plots compared to dry plots (61%), possibly due to the higher activity of β-glucosidase. Though mass loss at this final time point varied with both warming and precipitation treatments, the compound-specific degradation of litter captured by diffuse reflectance infra-red Fourier transform (DRIFT) and 13C Nuclear Magnetic Resonance (NMR) spectroscopy revealed that only the precipitation treatments significantly altered the chemistry of carbon compounds in the decomposed tissue. Litter that decomposed in the dry treatment had a higher proportion of carbohydrates remaining than litter in the wet and ambient treatments. Similarly, although ergosterol content and potential activity of phenol oxidase decreased in the warmer treatments, the consequences of this response were not observed in the degradation of specific compounds in litter, which varied only with precipitation treatments. Our results suggests that mass loss and enzyme activities may not accurately capture the complexity of compound-specific degradation of litter during decomposition. Our results also identified non-linear responses of β-glucosidase and N-acetyl-β-D-glucosaminidase (NAG) activities to warming. These results thus emphasize the complexities of litter decomposition and suggest that similar changes in decomposition across other grass species could alter the carbon budget of grasslands.

The influence of litter composition across the litter–soil interface on mass loss, nitrogen dynamics and the decomposer community

Many studies have investigated the influence of plant litter species composition on decomposition, but results have been context-dependent. Litter and soil are considered to constitute a decomposition continuum, but whether litter and soil ecosystems respond to litter identity and mixing in the same manner is unsure. In a field experiment utilizing 5 litter species and their mixture, we investigated whether the effects of litter identity and mixing on mass loss, nutrient dynamics, and decomposer communities are consistent across the litter–soil interface. In monoculture, mass loss and nitrogen (N) dynamics in the litter layer corresponded to the underlying soil N availability, demonstrating the continuum of resources from litter to soil. Litter microbial biomass and mesofauna abundance tended to be greater on litter with a faster decay rate and greater N release. However, soil decomposer abundance and diversity were not greater with higher soil N, causing litter and soil communities to respond differently to litter identity. Non-additive mass loss and N dynamics were observed after 6 months, and were correlated with non-additive litter microbial community composition and litter mesofauna communities, but all other aspects of the litter community and all measures of the soil community were additive. Decomposer communities and N dynamics did not respond similarly to the litter mixture across the litter–soil interface. This study is one of the few to comprehensively examine how a litter mixture influences decomposition dynamics and communities across the soil–litter interface, including multiple taxa and trophic levels. Our results demonstrate that processes associated with decomposition are decoupled for litter and soil, particularly in that litter showed non-additivity in mass loss, N release and decomposer community, but soil responses were largely additive.

The Use of Pyrosequencing to Analyze Microbial Populations in Poultry Management to Minimize Downstream Food Contamination

The use of antibiotics in animals grown for human consumption has been banned in many parts of the world and is becoming less favorable in the US. With less or no antibiotics fed, the risk of microbial contamination of food is higher when processed. In the current study, the objective was to identify and compare the effect of both ceca and litter microbial communities present before and after treatment. The treatments consisted of 1) challenging newborn chicks at 3 days and then again at 38 days with either Salmonella enteritidis or Campylobacter jejuni or no bacteria in the presence of or without probiotics added to the feed and 2) windrow composting or no composting of litter as part of poultry house management. Aseptically ceca and litter samples were collected and stored at 4°C until processed. Bacterial genomic DNA was isolated from both sets of samples using either the Promega SV Wizard Genomic DNA Purification kit (Ceca) or Zymo‐spin soil microbe DNA midiprep kit (litter). The DNA from each sample was then amplified using 16s universal forward and reverse primers containing the specific Roche defined library‐L specific sequences as well as Multiplex Identifiers (MID) to allow for automated software identification of the samples after pooling, multiplexing and sequencing. We report the bioinformatic pipeline and the microbial distributions at the genus and species level for each treatment.. Pyrosequencing can be used to obtain valid comparisons between effects of various treatments on pathogenic versus beneficial bacteria in growth and management of animals used for human consumption.Funding: Office of Research and Sponsored Projects, Stephen F. Austin State University; Ed and Gwen Cole, Nacogdoches, TX.

Effects of leaf litter consumption by millipedes (Harpaphe haydeniana) on subsequent decomposition depends on litter type

Most estimates of litter decomposition rates do not account well for the effects of soil macrofauna, and so may not accurately represent decomposition in ecosystems in which litter-transforming soil fauna are abundant. In coastal rainforests of British Columbia, Canada, millipedes are the dominant macrofauna and consume a substantial proportion of annual leaf litterfall, most of which is egested as faecal pellets. Little is known about the fate of millipede faecal pellets, which hinders accurate estimation of rates of litter decomposition in these ecosystems. We assessed the influence of feeding by the millipede (Harpaphe haydeniana) on decomposition of broadleaf (maple) and needle (Douglas-fir) litter by comparing rates of CO2 release during 56-day laboratory incubation from litter which had been ingested by millipedes and transformed into faecal pellets with that from unconsumed leaf litter. Changes in litter microbial communities as a consequence of millipede ingestion were assessed by comparing the PLFA profiles of uningested litter and faeces during incubation.Rates of CO2 release from litter and faeces were similar. CO2 release was greater in maple litter than Douglas-fir litter, and this difference persisted in faeces arising from the ingested litter. Maple litter had higher bacterial abundance and was dominated by Gram-negative bacteria; Douglas-fir litter was dominated by Gram-positive bacteria. Differences in bacterial abundances on the two litters were retained through millipede gut passage, but abundance of Gram-negative bacteria declined with gut passage of maple leaves, such that microbial communities were more similar in the two types of faeces. CO2 release was stimulated by grinding of litter and of faeces, indicating that enclosure of millipede faeces within pellets is partially responsible for the slow decomposition of this material. Similar decomposition rates of faeces and undigested litter indicate that effects of litter-transforming fauna such as millipedes on decomposition rates can be adequately accounted for in models by including estimates of the mass of litter assimilated.

Stoichiometric controls of nitrogen and phosphorus cycling in decomposing beech leaf litter

Resource stoichiometry (C:N:P) is an important determinant of litter decomposition. However, the effect of elemental stoichiometry on the gross rates of microbial N and P cycling processes during litter decomposition is unknown. In a mesocosm experiment, beech (Fagus sylvatica L.) litter with natural differences in elemental stoichiometry (C:N:P) was incubated under constant environmental conditions. After three and six months, we measured various aspects of nitrogen and phosphorus cycling. We found that gross protein depolymerization, N mineralization (ammonification), and nitrification rates were negatively related to litter C:N. Rates of P mineralization were negatively correlated with litter C:P. The negative correlations with litter C:N were stronger for inorganic N cycling processes than for gross protein depolymerization, indicating that the effect of resource stoichiometry on intracellular processes was stronger than on processes catalyzed by extracellular enzymes. Consistent with this, extracellular protein depolymerization was mainly limited by substrate availability and less so by the amount of protease. Strong positive correlations between the interconnected N and P pools and the respective production and consumption processes pointed to feed-forward control of microbial litter N and P cycling. A negative relationship between litter C:N and phosphatase activity (and between litter C:P and protease activity) demonstrated that microbes tended to allocate carbon and nutrients in ample supply into the production of extracellular enzymes to mine for the nutrient that is more limiting. Overall, the study demonstrated a strong effect of litter stoichiometry (C:N:P) on gross processes of microbial N and P cycling in decomposing litter; mineralization of N and P were tightly coupled to assist in maintaining cellular homeostasis of litter microbial communities.

Microbial Functional Diversity Associated with Plant Litter Decomposition Along a Climatic Gradient

Predicted changes in climate associated with increased greenhouse gas emissions can cause increases in global mean temperature and changes in precipitation regimes. These changes may affect key soil processes, e.g., microbial CO(2) evolution and biomass, mineralization rates, primary productivity, biodiversity, and litter decomposition, which play an important role in carbon and nutrient cycling in terrestrial ecosystems. Our study examined the changes in litter microbial communities and decomposition along a climatic gradient, ranging from arid desert to humid Mediterranean regions in Israel. Wheat straw litter bags were placed in arid, semi-arid, Mediterranean, and humid Mediterranean sites. Samples were collected seasonally over a 2-year period in order to evaluate mass loss, litter moisture, C/N ratio, bacterial colony-forming units (CFUs), microbial CO(2) evolution and biomass, microbial functional diversity, and catabolic profile. Decomposition rate was the highest during the first year of the study at the Mediterranean and arid sites. Community-level physiological profile and microbial biomass were the highest in summer, while bacterial CFUs were the highest in winter. Microbial functional diversity was found to be highest at the humid Mediterranean site, whereas substrate utilization increased at the arid site. Our results support the assumption that climatic factors control litter degradation and regulate microbial activity.

Microbial activity and quality changes during decomposition of Quercus ilex leaf litter in three Mediterranean woods

Changes in enzyme activities during litter decomposition provide diagnostic information on the dynamics of decay and functional microbial succession. Here we report a comparative study of enzyme activities involved in the breakdown of major plant components and of other key parameters (microbial respiration, fungal biomass, N, lignin and cellulose contents) in homogeneous leaf litter of Quercus ilex L. incubated in three evergreen oak woods in Southern Italy (Campania), differing for chemical and physical soil characteristics and microclimatic conditions. The results showed that the litter mass loss rates were similar in the three wood sites. Independently of the incubation sites, cellulase, xylanase and peroxydase activities showed seasonal variations with maximum and minimum levels in wet and dry periods, respectively, and this pattern closely matched microbial respiration. Activities of α- and β-amylase, instead, were high at the beginning of incubation and quickly decreased with decomposition progress because their substrate was rapidly depleted. Laccase activity, in contrast, was low at the beginning of incubation but after 6 months it increased significantly. The increase of laccase activity was correlated to an increase in fungal biomass, probably reflecting a major shift in the litter microbial community. As concerns quality changes, N and lignin content did not significantly change during decay. The cellulosic component started being degraded after about 6 months in the litter incubated in two of the three wood sites and from the start of decomposition in the third site. Apart from minor differences in the levels of certain enzyme activities, the data showed that the functional microbial succession involved in the decomposition of Q. ilex leaf litter did not change appreciably in response to differences in soil and microclimatic conditions in the incubation sites.

The Effect of Alum Addition on Microbial Communities in Poultry Litter

Alum [Al2(SO4)3·14H2 O] is a common poultry litter amendment used to decrease water-soluble phosphorus or reduce ammonia volatilization, or both. Although the physiochemical effects of alum addition have been well researched, little attention has been given to the poultry litter microbial communities. The goal of this study was to use molecular biological methods [denaturing gradient gel electrophoresis (DGGE), community cloning, and quantitative real-time PCR] to characterize general, group-specific and pathogenic microbial communities in alum (10% wt/wt) and non-alum-treated litter. According to quantitative real-time PCR analyses, alum addition to the poultry litter resulted in significant reductions in both Campylobacter jejuni and Escherichia coli concentrations by the end of the first month of the experiment (3 log and 2 log, respectively). The concentrations of Salmonella spp. were below detection (<5 × 103 cell·g−1 of litter) for the entire experiment. The DGGE analyses revealed significant reductions in the Clostridium/Eubacterium and low %GC gram-positive groups in the alum-treated litters by the end of the first month, with no bands detectable for either group after 8 wk of incubation. Conversely, minimal effects of alum addition were observed in the Actinomycetes community. The most significant shift in the microbial community (based on DGGE analyses) occurred in the fungal population, with a large increase in diversity and abundance within 1 mo of alum addition (1 dominant band on d 0 to 9 dominant bands at 4 wk). Specifically, the incidence of Aspergillus spp. increased from 0 to 50% of the sequences in fungal clone libraries (n = 80) over the course of the experiment. This suggests that the addition of alum to poultry litter potentially shifts the microbial populations from bacterially dominated to dominated by fungi. The ramifications of this shift in dominance are still unknown, and future work will be aimed at characterizing these fungi and elucidating their role in the acidified litter environment.