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Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N 2 O - is intricately controlled by O 2 . While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N 2 O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O 2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O 2 legacy for accurately predicting N 2 O emissions originating from denitrification., (© 2024. The Author(s).)

Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks., Competing Interests: There are no competing interests, (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f 4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Even though drought impacts on tree physiology have been identified, whether drought affects leaf litter chemistry that, in turn, influences litter decay rates is still poorly understood. We compared litter quality and decomposition for two cohorts of leaves from five co-occurring seasonally deciduous tree species: Acer saccharum, Tilia americana, Quercus rubra, Quercus alba, and Ostrya virginiana. One cohort experienced a growing-season drought, and the other cohort came from the same trees in the ensuing, post-drought growing season. Leaf litter production was greater for drought litter than post-drought litter for all five species. Specific leaf area and nitrogen concentrations were 20% greater for the drought cohort than the post-drought cohort. Concentrations of non-structural carbohydrates were about 14% greater for the drought cohort, except for greater values for post-drought A. saccharum litter. Pectin in the middle lamella of leaf litter was 31% lower for the drought cohort compared to post-drought cohort. We found few differences in litter decay rates between drought and post-drought cohorts, although Q. rubra litter had more decomposition for the post-drought cohort than the drought cohort, whereas A. saccharum litter had more decomposition for the drought cohort than the post-drought cohort. Leaf litter decay rates for the drought cohort were related to litter nitrogen and lignin concentrations, whereas decay rates for the post-drought cohort were related to litter carbohydrate concentrations. Our findings suggest that the role of drought events on seasonally deciduous forest ecosystems must recognize species-specific, idiosyncratic responses in leaf litter quality and decomposition., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here, we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analysed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

Sphagnum peat mosses have an extraordinary impact on the global carbon cycle as they control long-term carbon sequestration in boreal peatland ecosystems. Sphagnum species engineer peatlands, which harbour roughly a quarter of all terrestrial carbon, through peat accumulation by constructing their own niche that allows them to outcompete other plants. Interspecific variation in peat production, largely resulting from differences in tissue decomposability, is hypothesized to drive niche differentiation along microhabitat gradients thereby alleviating competitive pressure. However, little empirical evidence exists for the role of selection in the creation and maintenance of such gradients. In order to document how niche construction and differentiation evolved in Sphagnum , we quantified decomposability for 54 species under natural conditions and used phylogenetic comparative methods to model the evolution of this carbon cycling trait. We show that decomposability tracks the phylogenetic diversification of peat mosses, that natural selection favours different levels of decomposability corresponding to optimum niche and that divergence in this trait occurred early in the evolution of the genus prior to the divergence of most extant species. Our results demonstrate the evolution of ecosystem engineering via natural selection on an extended phenotype, of a fundamental ecosystem process, and one of the Earth's largest soil carbon pools.

Northern peatlands are experiencing more frequent and severe fire events as a result of changing climate conditions. Recent studies show that such a fire-regime change imposes a direct climate-warming impact by emitting large amounts of carbon into the atmosphere. However, the fires also convert parts of the burnt biomass into pyrogenic carbon. Here, we show a potential climate-cooling impact induced by fire-derived pyrogenic carbon in laboratory incubations. We found that the accumulation of pyrogenic carbon reduced post-fire methane production from warm (32 °C) incubated peatland soils by 13-24%. The redox-cycling, capacitive, and conductive electron transfer mechanisms in pyrogenic carbon functioned as an electron snorkel, which facilitated extracellular electron transfer and stimulated soil alternative microbial respiration to suppress methane production. Our results highlight an important, but overlooked, function of pyrogenic carbon in neutralizing forest fire emissions and call for its consideration in the global carbon budget estimation.

Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.

Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH 4 ). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO 2 ) and CH 4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

Ticks are widespread vectors for many important medical and veterinary infections, and a better understanding of the factors that regulate their population dynamics is needed to reduce risk for humans, wildlife, and domestic animals. Most ticks, and all non-nidicolous tick species, spend only a small fraction of their lives associated with vertebrate hosts, with the remainder spent in or on soils and other substrates. Ecological studies of tick-borne disease dynamics have emphasized tick-host interactions, including host associations, burdens, and efficiencies of pathogen transmission, while under emphasizing tick biology during off-host periods. Our ability to predict spatiotemporal trends in tick-borne diseases requires more knowledge of soil ecosystems and their effect on host and tick populations. In this review, we focus on tick species of medical and veterinary concern and describe: 1) the relationships between soil factors and tick densities; 2) biotic and abiotic factors within the soil ecosystem that directly affect tick survival; 3) potential indirect effects on ticks mediated by soil ecosystem influences on their vertebrate hosts; 4) the potential for tick-mediated effects on vertebrate host populations to affect ecosystems; and 5) possible nontarget impacts of tick management on the soil ecosystem. Soils are complex ecosystem components with enormous potential to affect the survival and behavior of ticks during their off-host periods. Hence, tick-borne disease systems present an excellent opportunity for soil ecologists and public health researchers to collaborate and improve understanding of these medically important and ecologically complex disease cycles., (© The Author(s) 2019. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The blacklegged tick (Ixodes scapularis) spends up to 10 months in the soil between feeding as larvae and questing for hosts as nymphs the following year. We tracked the survival and energy use of 4320 engorged larvae evenly divided across 288 microcosms under field conditions from September to July on sites with high (>12 nymphs/150 m2) and low (<1.2 nymphs/150 m2) densities of naturally questing I. scapularis in New York State. Subsets of microcosms were destructively sampled periodically during this period to determine tick survivorship and physiological age. Across all sites tick mortality was low during the winter and increased in the spring and early summer, coincident with increasing energy use. Neither energy use nor mortality differed significantly between sites with high vs low natural tick density, but we did observe a significant positive relationship between soil organic matter content and the survival of I. scapularis during the spring. Our results suggest that the off-host mortality and energy use of I. scapularis nymphs is relatively low in the winter and increases significantly in the spring and early summer.

We present a meta-analysis of plant responses to fertilization experiments conducted in lowland, species-rich, tropical forests. We also update a key result and present the first species-level analyses of tree growth rates for a 15-yr factorial nitrogen (N), phosphorus (P), and potassium (K) experiment conducted in central Panama. The update concerns community-level tree growth rates, which responded significantly to the addition of N and K together after 10 yr of fertilization but not after 15 yr. Our experimental soils are infertile for the region, and species whose regional distributions are strongly associated with low soil P availability dominate the local tree flora. Under these circumstances, we expect muted responses to fertilization, and we predicted species associated with low-P soils would respond most slowly. The data did not support this prediction, species-level tree growth responses to P addition were unrelated to species-level soil P associations. The meta-analysis demonstrated that nutrient limitation is widespread in lowland tropical forests and evaluated two directional hypotheses concerning plant responses to N addition and to P addition. The meta-analysis supported the hypothesis that tree (or biomass) growth rate responses to fertilization are weaker in old growth forests and stronger in secondary forests, where rapid biomass accumulation provides a nutrient sink. The meta-analysis found no support for the long-standing hypothesis that plant responses are stronger for P addition and weaker for N addition. We do not advocate discarding the latter hypothesis. There are only 14 fertilization experiments from lowland, species-rich, tropical forests, 13 of the 14 experiments added nutrients for five or fewer years, and responses vary widely among experiments. Potential fertilization responses should be muted when the species present are well adapted to nutrient-poor soils, as is the case in our experiment, and when pest pressure increases with fertilization, as it does in our experiment. The statistical power and especially the duration of fertilization experiments conducted in old growth, tropical forests might be insufficient to detect the slow, modest growth responses that are to be expected., (© 2018 by the Ecological Society of America.)

Model denitrifiers convert NO3- to N 2 , but it appears that a significant fraction of natural populations are truncated, conducting only one or two steps of the pathway. To better understand the diversity of partial denitrifiers in soil and whether discrepancies arise between the presence of known N-oxide reductase genes and phenotypic features, bacteria able to reduce NO3- to NO2- were isolated from soil, N-oxide gas products were measured for eight isolates, and six were genome sequenced. Gas phase analyses revealed that two were complete denitrifiers, which genome sequencing corroborated. The remaining six accumulated NO and N 2 O to varying degrees and genome sequencing of four indicated that two isolates held genes encoding nitrate reductase as the only dissimilatory N-oxide reductase, one contained genes for both nitrate and nitric oxide reductase, and one had nitrate and nitrite reductase. The results demonstrated that N-oxide production was not always predicted by the genetic potential and suggested that partial denitrifiers could be readily isolated among soil bacteria. This supported the hypothesis that each N-oxide reductase could provide a selectable benefit on its own, and therefore, reduction of nitrate to dinitrogen may not be obligatorily linked to complete denitrifiers but instead a consequence of a functionally diverse community., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H 2 -CO 2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H + rather than Na + transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na + and H + chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

We explored the relationship between the diversity and abundance of the soil arthropod predator community and the overwinter survival of engorged larval Ixodes scapularis Say under variable snow cover in a hardwood forest. We reduced the snow cover over 30 soil core field microcosms, simulating predicted changes in snow pack in the northeastern United States. An additional 29 microcosms were used as references with no snow pack manipulation. Each microcosm contained 15 engorged larval I. scapularis. We expected lower soil temperature without insulating snow cover to reduce tick survival. However, we observed that reduced snow cover had no effect, with 44.2 and 44.7% overwintering successfully in the reference and snow-removal plots, respectively. Increasing taxonomic family richness of arthropod predators and the total number of large (>1 mm) arthropod predators significantly reduced the overwinter survivorship of I. scapularis within the microcosms. Small (<1 mm) arthropod predator abundance had no effect. Our results suggest that forests with complex natural arthropod predator communities show reduced tick survival., (© The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T), a methanogen isolated from a minerotrophic fen. This is the first genome report of the Methanosphaerula genus, within the Methanoregulaceae family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide range of ecological and geographical settings., (Copyright © 2015 Cadillo-Quiroz et al.)

Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.

Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1% SDS. Cell size was 0.6×1.5-2.8 µm for strain SWAN1T and 0.45-0.85×1.5-35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32-37 °C, and their growth spanned through a slightly low to neutral pH range (4.7-7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4-5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01-0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus Methanobacterium. Strain SWAN1T shared 94-97% similarity with the type strains of recognized species of the genus Methanobacterium, whereas strain AL-21 shared 99% similarity with Methanobacterium lacus 17A1T. On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1T (=DSM 25820T=JCM 18151T) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of Methanobacterium lacus.

The integration of ecology and evolutionary biology requires an understanding of the evolutionary lability in species' ecological niches. For tropical trees, specialization for particular soil resource and topographic conditions is an important part of the habitat niche, influencing the distributions of individual species and overall tree community structure at the local scale. However, little is known about how these habitat niches are related to the evolutionary history of species. We assessed the relationship between taxonomic rank and tree species' soil resource and topographic niches in eight large (24-50 ha) tropical forest dynamics plots. Niche overlap values, indicating the similarity of two species' distributions along soil or topographic axes, were calculated for all pairwise combinations of co-occurring tree species at each study site. Congeneric species pairs often showed greater niche overlap (i.e., more similar niches) than non-congeneric pairs along both soil and topographic axes, though significant effects were found for only five sites based on Mantel tests. No evidence for taxonomic effects was found at the family level. Our results indicate that local habitat niches of trees exhibit varying degrees of phylogenetic signal at different sites, which may have important ramifications for the phylogenetic structure of these communities.

Tropical tree communities are shaped by local-scale habitat heterogeneity in the form of topographic and edaphic variation, but the life-history stage at which habitat associations develop remains poorly understood. This is due, in part, to the fact that previous studies have not accounted for the widely disparate sample sizes (number of stems) that result when trees are divided into size classes. We demonstrate that the observed habitat structuring of a community is directly related to the number of individuals in the community. We then compare the relative importance of habitat heterogeneity to tree community structure for saplings, juveniles and adult trees within seven large (24-50 ha) tropical forest dynamics plots while controlling for sample size. Changes in habitat structuring through tree life stages were small and inconsistent among life stages and study sites. Where found, these differences were an order of magnitude smaller than the findings of previous studies that did not control for sample size. Moreover, community structure and composition were very similar among tree sub-communities of different life stages. We conclude that the structure of these tropical tree communities is established by the time trees are large enough to be included in the census (1 cm diameter at breast height), which indicates that habitat filtering occurs during earlier life stages.

Peatlands are an important source of the atmospheric greenhouse gas methane (CH4). Although CH4 cycling and fluxes have been quantified for many northern peatlands, imprecision in process-based approaches to predicting CH4 emissions suggests that our understanding of underlying processes is incomplete. Microbial anaerobic oxidation of CH4 (AOM) is an important CH4 sink in marine sediments, but AOM has only recently been identified in a few nonmarine systems. We used (13)C isotope tracers and followed the fate of (13)C into CO2 and peat in order to study the geographic extent, relative importance, and biogeochemistry of AOM in 15 North American peatlands spanning a ∼1500 km latitudinal transect that varied in hydrology, vegetation, and soil chemistry. For the first time, we demonstrate that AOM is a widespread and quantitatively important process across many peatland types and that anabolic microbial assimilation of CH4-C occurs. However, AOM rate is not predicted by CH4 production rates and the primary mechanism of C assimilation remains uncertain. AOM rates are higher in fen than bog sites, suggesting electron acceptor constraints on AOM. Nevertheless, AOM rates were not correlated with porewater ion concentrations or stimulated following additions of nitrate, sulfate, or ferric iron, suggesting that an unidentified electron acceptor(s) must drive AOM in peatlands. Globally, we estimate that AOM could consume a large proportion of CH4 produced annually (1.6-49 Tg) and thereby constrain emissions and greenhouse gas forcing.

To examine the mechanisms of earthworm effects on forest soil C and N, we double-labeled leaf litter with 13C and 15N, applied it to sugar maple forest plots with and without earthworms, and traced isotopes into soil pools. The experimental design included forest plots with different earthworm community composition (dominated by Lumbricus terrestris or L. rubellus). Soil carbon pools were 37% lower in earthworm-invaded plots largely because of the elimination of the forest floor horizons, and mineral soil C:N was lower in earthworm plots despite the mixing of high C:N organic matter into soil by earthworms. Litter disappearance over the first winter-spring was highest in the L. terrestris (T) plots, but during the warm season, rapid loss of litter was observed in both L. rubellus (R) and T plots. After two years, 22.0% +/- 5.4% of 13C released from litter was recovered in soil with no significant differences among plots. Total recovery of added 13C (decaying litter plus soil) was much higher in no-worm (NW) plots (61-68%) than in R and T plots (20-29%) as much of the litter remained in the former whereas it had disappeared in the latter. Much higher percentage recovery of 15N than 13C was observed, with significantly lower values for T than R and NW plots. Higher overwinter earthworm activity in T plots contributed to lower soil N recovery. In earthworm-invaded plots isotope enrichment was highest in macroaggregates and microaggregates whereas in NW plots silt plus clay fractions were most enriched. The net effect of litter mixing and priming of recalcitrant soil organic matter (SOM), stabilization of SOM in soil aggregates, and alteration of the soil microbial community by earthworm activity results in loss of SOM and lowering of the C:N ratio. We suggest that earthworm stoichiometry plays a fundamental role in regulating C and N dynamics of forest SOM.

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24-50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9-34% and 5-29%, respectively), and all environmental variables together explain 13-39% of compositional variation within a plot. A large fraction of variation (19-37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe.

Fluctuating environmental conditions can promote diversity and control dominance in community composition. In addition to seasonal temperature and moisture changes, seasonal supply of metabolic substrates selects populations temporally. Here we demonstrate cascading effects in the supply of metabolic substrates on methanogenesis and community composition of anaerobic methanogenic archaea in three contrasting peatlands in upstate New York. Fresh samples of peat soils, collected about every 3 months for 20 months and incubated at 22 ± 2°C regardless of the in situ temperature, exhibited potential rates of methane (CH(4)) production of 0.02-0.2 mmol L(-1) day(-1) [380-3800 nmol g(-1) (dry) day(-1)). The addition of acetate stimulated rates of CH(4) production in a fen peatland soil, whereas addition of hydrogen (H(2)), and simultaneous inhibition of H(2)-consuming acetogenic bacteria with rifampicin, stimulated CH(4) production in two acidic bog soils, especially, in autumn and winter. The methanogenic community structure was characterized using T-RFLP analyses of SSU rRNA genes. The E2 group of methanogens (Methanoregulaceae) dominated in the two acidic bog peatlands with relatively greater abundance in winter. In the fen peatland, the E1 group (Methanoregulaceae) and members of the Methanosaetaceae were co-dominant, with E1 having a high relative abundance in spring. Change in relative abundance profiles among methanogenic groups in response to added metabolic substrates was as predicted. The acetate-amendment increased abundance of Methanosarcinaceae, and H(2)-amendment enhanced abundance of E2 group in all peat soils studied, respectively. Additionally, addition of acetate increased abundance of Methanosaetaceae only in the bog soils. Variation in the supply of metabolic substrates helps explain the moderate diversity of methanogens in peatlands.

The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.

We maintained a factorial nitrogen (N), phosphorus (P), and potassium (K) addition experiment for 11 years in a humid lowland forest growing on a relatively fertile soil in Panama to evaluate potential nutrient limitation of tree growth rates, fine-litter production, and fine-root biomass. We replicated the eight factorial treatments four times using 32 plots of 40 x 40 m each. The addition of K was associated with significant decreases in stand-level fine-root biomass and, in a companion study of seedlings, decreases in allocation to roots and increases in height growth rates. The addition of K and N together was associated with significant increases in growth rates of saplings and poles (1-10 cm in diameter at breast height) and a further marginally significant decrease in stand-level fine-root biomass. The addition of P was associated with a marginally significant (P = 0.058) increase in fine-litter production that was consistent across all litter fractions. Our experiment provides evidence that N, P, and K all limit forest plants growing on a relatively fertile soil in the lowland tropics, with the strongest evidence for limitation by K among seedlings, saplings, and poles.

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8(T), was isolated from an acidic (pH 4.0-4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2-0.3 μm in diameter and 0.8-3.0 μm long) and irregular cocci (0.2-0.8 μm in diameter). The culture utilized H(2)/CO(2) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na(+) and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8(T) is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8(T) (=DSM 21154(T) =JCM 14090(T)).

Plant root exudates increase nutrient availability and influence microbial communities including archaeal members. We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the rhizoplane, MS was dominant on both plants although as a less variable fraction in S. purpurea. RC-I was significantly more abundant than E2 on S. purpurea, while the opposite was observed on D. arundinaceum, suggesting a plant-specific enrichment. Also, the statistical analyses of T-RFLP data showed that although both plants overlap in their community structure, factors such as plant type, patch location, and time could explain nearly a third of the variability in the dataset. Other factors such as water table, plant replicate, and root depth had a low contribution to the observed variance. The results of this study illustrate the general effects of roots and the specific effects of plant types on their nearby archaeal communities which in bog-inhabiting plants were mainly composed by methanogenic groups.

Peatlands are important sources of CH(4) emissions to the atmosphere and molecular surveys have identified a diverse, but mainly uncultured, euryarchaeal community in them. Characterization of a strain, E1-9c(T), associated with uncultured group E1, from a minerotrophic fen is reported. Cells were regular cocci, usually found in pairs, that stained Gram-positive and were resistant to lysis by 0.1 % SDS. Multiple flagella were observed, but motility was not observed in wet mounts. Optimal growth was obtained at moderate temperatures (28-30 degrees C) and slightly acidic pH (5.5). Total Na(+) and NaCl were only tolerated at concentrations less than 100 mM and 0.5 %, respectively, and Na(2)S concentrations above 0.1 mM were inhibitory. H(2)/CO(2) and formate were the only methanogenic substrates used by E1-9c(T); formate concentrations above 50 mM were inhibitory for growth. Vitamins, coenzyme M and acetate (4 mM) were required for growth and the doubling time was about 19 h. Phylogenetic analysis of the 16S rRNA gene and inferred McrA amino acid sequences showed that E1-9c(T) represented an independent lineage within the order Methanomicrobiales. Physiological and phylogenetic comparisons with different members of the order supported classification of E1-9c(T) in a new genus in the Methanomicrobiales. The name Methanosphaerula palustris gen. nov., sp. nov. is proposed; strain E1-9c(T) (=ATCC BAA-1565(T) =DSM 19958(T)) is the type strain of Methanosphaerula palustris.

Minerotrophic fen peatlands are widely distributed in northern latitudes and, because of their rapid turnover of organic matter, are potentially larger sources of atmospheric methane than bog peatlands per unit area. However, studies of the archaeal community composition in fens are scarce particularly in minerotrophic sites. Several 16S rRNA-based primer sets were used to obtain a broad characterization of the archaeal community in a minerotrophic fen in central New York State. A wide archaeal diversity was observed in the site: 11 euryarchaeal and 2 crenarchaeal groups, most of which were uncultured. The E1 group, a novel cluster in the order Methanomicrobiales, and Methanosaetaceae were the codominant groups in all libraries and results of terminal restriction fragment length polymorphism (T-RFLP) analysis. Given its abundance and potential hydrogenotrophic methane contribution, the E1 group was targeted for culture attempts with a low-ionic-strength medium (PM1). Initial attempts yielded Methanospirillum-dominated cultures. However, by incorporating a T-RFLP analysis as a quick selection tool for treatments and replicates, we were able to select an enrichment dominated by E1. Further dilutions to 10(-9) and tracking with T-RFLP yielded a strain named E1-9c. E1-9c is a novel coccoid hydrogenotrophic, mesophilic, slightly acidophilic methanogen and is highly sensitive to Na(2)S concentrations (requires <0.12 mM for growth). We propose E1-9c as the first representative of a novel genus in the Methanomicrobiales order.

To explore the importance of 12 elements in litter production and decomposition, we fertilized 36 1600 m(2)-plots with combinations of N, P, K, or micronutrients (i.e. B, Ca, Cu, Fe, Mg, Mn, Mo, S, Zn) for 6 years in a lowland Panamanian forest. The 90% of litter falling as leaves and twigs failed to increase with fertilization, but reproductive litter (fruits and flowers) increased by 43% with N. K enhanced cellulose decomposition; one or more micronutrients enhanced leaf-litter decomposition; P enhanced both. Our results suggest tropical forests are a non-Liebig world of multiple nutrient limitations, with at least four elements shaping rates of litterfall and decomposition. Multiple metallomic enzymes and cofactors likely create gradients in the break down of leaf litter. Selection favours individuals that make more propagules, and even in an N-rich forest, N is a non-substitutable resource for reproduction.

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

Two methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one methanogen and two bacterial sequences. The methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family methanogens.

Acidic peatlands are among the largest natural sources of atmospheric methane and harbour a large diversity of methanogenic Archaea. Despite the ubiquity of methanogens in these peatlands, indigenous methanogens capable of growth at acidic pH values have resisted culture and isolation; these recalcitrant methanogens include members of an uncultured family-level clade in the Methanomicrobiales prevalent in many acidic peat bogs in the Northern Hemisphere. However, we recently succeeded in obtaining a mixed enrichment culture of a member of this clade. Here we describe its isolation and initial characterization. We demonstrate that the optimum pH for methanogenesis by this organism is lower than that of any previously described methanogen.

A field study was conducted to evaluate the effects of exotic earthworm invasions on the rates of leaf litter disappearance in a northern hardwood forest in southcentral New York, USA. Specifically, we assessed whether differences in litter quality and the species composition of exotic earthworm communities affected leaf litter disappearance rates. Two forest sites with contrasting communities of exotic earthworms were selected, and disappearance rates of sugar maple and red oak litter were estimated in litter boxes in adjacent earthworm-free, transition, and earthworm-invaded plots within each site. After 540 days in the field, 1.7-3 times more litter remained in the reference plots than in the earthworm-invaded plots. In the earthworm-invaded plots, rates of disappearance of sugar maple litter were higher than for oak litter during the first year, but by the end of the experiment, the amount of sugar maple and oak litter remaining in the earthworm-invaded plots was identical within each site. The composition of the earthworm communities significantly affected the patterns of litter disappearance. In the site dominated by the anecic earthworm Lumbricus terrestris and the endogeic Aporrectodea tuberculata, the percentage of litter remaining after 540 days (approximately 17%) was significantly less than at the site dominated by L. rubellus and Octolasion tyrtaeum (approximately 27%). This difference may be attributed to the differences in feeding behavior of the two litter-feeding species: L. terrestris buries entire leaves in vertical burrows, whereas L. rubellus usually feeds on litter at the soil surface, leaving behind leaf petioles and veins. Our results showed that earthworms not only accelerate litter disappearance rates, but also may reduce the differences in decomposition rates that result from different litter qualities at later stages of decay. Similarly, our results indicate that earthworm effects on decomposition vary with earthworm community composition. Furthermore, because earthworm invasion can involve a predictable shift in community structure along invasion fronts or through time, the community dynamics of invasion are important in predicting the spatial and temporal effects of earthworm invasion on litter decomposition, especially at later stages of decay.

It is now understood that alterations in the species composition of soil organisms can lead to changes in aboveground communities. In this study, we assessed the importance of spatial scale and forest size on changes in arbuscular mycorrhizal fungal (AMF) spore communities by sampling AMF spores in soils of forested mainland and island sites in the vicinity of Gatun Lake, Republic of Panama. We encountered a total of 27 AMF species or morphospecies, with 17, 8, 1 and 1 from the genera Glomus, Acaulospora, Sclerosystis, and Scutellospora, respectively. At small scales (<100 m2), we found little evidence for spatial structuring of AMF communities (decay of Morisita-Horn community similarity with distance). However, at large spatial scales, we found that the AMF spore community of a mainland plot was more similar to other mainland plots several kilometers (>5) away than to nearby island plots (within 0.7 km). Likewise, most island plots were more similar to other island plots regardless of geographic separation. There was no decay in AMF species richness (number of species), or Shannon diversity (number of species and their spore numbers) either with decreasing forest-fragment size, or with decreasing plant species richness. Of the six most common species that composed almost 70% of the total spore volume, spores of Glomus "tsh" and G. clavisporum were more common in soils of mainland plots, while spores of Glomus "small brown" and Acaulospora mellea were more abundant in soils of island plots. None of these common AMF species showed significant associations with soil chemistry or plant diversity. We suggest that the convergence of common species found in AMF spore communities in soils of similar forest sizes was a result of forest fragmentation. Habitat-dependent convergence of AMF spore communities may result in differential survival of tree seedlings regenerating on islands versus mainland.

Isoprene (2-methyl-1,3 butadiene) is a low-molecular-weight hydrocarbon emitted in large quantities to the atmosphere by vegetation and plays a large role in regulating atmospheric chemistry. Until now, the atmosphere has been considered the only significant sink for isoprene. However, in this study we performed both in situ and in vitro experiments with soil from a temperate forest near Ithaca, N.Y., that indicate that the soil provides a sink for atmospheric isoprene and that the consumption of isoprene is carried out by microorganisms. Consumption occurred rapidly in field chambers (672.60 +/- 30.12 to 2,718.36 +/- 86.40 pmol gdw day) (gdw is grams [dry weight] of soil; values are means +/- standard deviations). Subsequent laboratory experiments confirmed that isoprene loss was due to biological processes: consumption was stopped by autoclaving the soil; consumption rates increased with repeated exposure to isoprene; and consumption showed a temperature response consistent with biological activity (with an optimum temperature of 30 degrees C). Isoprene consumption was diminished under low oxygen conditions (120 +/- 7.44 versus 528.36 +/- 7.68 pmol gdw day under ambient O(2) concentrations) and showed a strong relationship with soil moisture. Isoprene-degrading microorganisms were isolated from the site, and abundance was calculated as 5.8 x 10 +/- 3.2 x 10 cells gdw. Our results indicate that soil may provide a significant biological sink for atmospheric isoprene.