Methane in West Siberia terrestrial seeps: Origin,transport, and metabolic pathways of production

The expansive plains of West Siberia contain globally significant carbon stocks, with Earth's most extensive peatland complex overlying the world's largest-known hydrocarbon basin. Numerous terrestrial methane seeps have recently been discovered on this landscape, located along the floodplains of the Ob and Irtysh Rivers in hotspots covering more than 2500 km². We articulated three hypotheses to explain the origin and migration pathways of methane within these seeps: (H1) uplift of Cretaceous-aged methane from deep petroleum reservoirs along faults and fractures, (H2) release of Oligocene-aged methane capped or trapped by degrading permafrost, and (H3) horizontal migration of Holocene-aged methane from surrounding peatlands. We tested these hypotheses using a range of geochemical tools on gas and water samples extracted from seeps, peatlands, and aquifers across the 120,000 km² study area. Seep-gas composition, radiocarbon age, and stable isotope fingerprints favor the peatland hypothesis of seep-methane origin (H3). Organic matter in raised bogs is the primary source of seep methane, but observed variability in stable isotope composition and concentration suggest production in two divergent biogeochemical settings that support distinct metabolic pathways of methanogenesis. Comparison of these parameters in raised bogs and seeps indicates that the first is bogs, via CO₂ reduction methanogenesis. The second setting is likely groundwater, where dissolved organic carbon from bogs is degraded via chemolithotrophic acetogenesis followed by acetate fermentation methanogenesis. Our findings highlight the importance of methane lateral migration in West Siberia's bog-dominated landscapes via intimate groundwater connections. The same phenomenon could occur in similar landscapes across the boreal-taiga biome, thereby making groundwater-fed rivers and springs potent methane sources.     

产甲烷常温古细菌和嗜热古细菌代谢网络拓扑结构与功能间的关联性研究

根据从KEGG数据库获得的产甲烷的常温古细菌Methanosarcina acetivorans(MAC)和嗜热古细菌Methanopyrus kandleri(MKA)的代谢网络,通过不同的网络属性特征的比较,发现常温古细菌MAC的代谢网络比嗜热古细菌MKA有更长的平均路径长度,更大的直径,这表明常温古细菌MAC的总体结构是相对低密度、松散的网络结构.同时为了从系统水平上分析这些特征蕴含的功能意义,采用了Grivan和Newman提出的模块算法(简称GN算法)分析这两个生物体的功能模块,并将所得的结果与KEGG数据库中的途径信息进行比较研究,发现大部分模块对应2~4个KEGG途径,表明这些网络模块均具有一定功能意义.     

The phylogenetic positions of three Basal-hexapod groups (protura, diplura, and collembola) based on ribosomal RNA gene sequences

This study combined complete 18S with partial 28S ribosomal RNA gene sequences ( approximately 2,000 nt in total) to investigate the relations of basal hexapods. Ten species of Protura, 12 of Diplura, and 10 of Collembola (representing all subgroups of these three clades) were sequenced, along with 5 true insects and 8 other arthropods, which served as out-groups. Trees were constructed with maximum parsimony, maximum likelihood, Bayesian analysis, and minimum-evolution analysis of LogDet-transformed distances. All methods yielded strong support for a clade of Protura plus Diplura, here named Nonoculata, and for monophyly of the Diplura. Parametric-bootstrapping analysis showed our data to be inconsistent with previous hypotheses (P < 0.01) that joined Protura with Collembola (Ellipura), that said Diplura are sister to true insects or are diphyletic, and that said Collembola are not hexapods. That is, our data are consistent with hexapod monophyly and Collembola grouped weakly with "Protura + Diplura" under most analytical conditions. As a caveat to the above conclusions, the sequences showed nonstationarity of nucleotide frequencies across taxa, so the CG-rich sequences of the diplurans and proturans may have grouped together artifactually; however, the fact that the LogDet method supported this group lessens this possibility. Within the basal hexapod groups, where nucleotide frequencies were stationary, traditional taxonomic subgroups generally were recovered: i.e., within Protura, the Eosentomata and Acerentomata (but Sinentomata was not monophyletic); within Collembola, the Arthropleona, Poduromorpha, and Entomobryomorpha (but Symphypleona was polyphyletic); and in Diplura, the most complete data set (> 2,100 nt) showed monophyly of Campodeoidea and of Japygoidea, and most methods united Projapygoidea with Japygoidea.     

Recovery of Methanogenesis Following Summer Drought in Soils from Two Cool Temperate Peatlands,New York State,USA

Following a summer drought, intact cores of peat soil from two cool temperate peatlands (a rain-fed bog and a groundwater-fed swamp) were exposed experimentally to three different water table levels. The goal was to examine recovery of anaerobic methanogenesis and to evaluate peat soil decomposition to methane (CH₄), carbon dioxide (CO₂), and dissolved organic carbon (DOC) upon rewetting. Methane emission from soils to the atmosphere was greatest (mean = 80 μmol m^?2 s^?1) when the entire peat core was rewetted quickly; emission was negligible at low water level and when peat cores were rewetted gradually. Rates of CO₂ emission (mean = 1.0 μmol m^?2 s^?1) were relatively insensitive to water level. Concentrations of CH₄ in soil air spaces suggest that onset of methanogenesis induces, but later represses, aerobic oxidation of CH₄ above the water table. Concentrations of CO₂ suggest production at the soil surface of swamp peat versus at greater depths in bog peat. Portions of peat soil incubated in vitro without oxygen (O₂) exhibited a lag before the onset of methanogenesis, and the lag time was less in peat from the cores rewetted quickly. The inhibition of methanogenesis by the selective inhibitor 2-bromoethanesulfonic acid (BES) decreased CO₂ production by 20 to 30% but resulted in an increase in concentrations of DOC by 2 to 5 times. The results show that methanogens in peat soils tolerate moderate drought, and recovery varies among different peat types. In peat soils, the inhibition of methanogenesis might enhance DOC availability.     

Control of Methane Metabolism in a Forested Northern Wetland,New York State,by Aeration,Substrates, and Peat Size Fractions

Although many northern peat-forming wetlands (peatlands) are a suitable habitat for anaerobic CH 4 -producing bacteria (methanogens), net CH 4 fluxes are typically low in forested systems. We examined whether soil factors (aeration, substrate availability, peat size fractions) constrained net CH 4 production in peat from a Sphagnum -moss dominated, forested peatland in central New York State. The mean rate of net CH 4 production measured at 24° C was 79 nmol g -1 d -1 , and the mean rate of CO 2 production (respiration) was 5.7 w mol g -1 d -1 , in surface (0 to 10 cm) and subsurface (30 to 40 cm) peat. Saturated peat (900% water content) exposed to oxic conditions for 2 days or 14 days showed no net CH 4 production when subsequently exposed to anoxic conditions. Rates of CO 2 production, measured concomitantly, were essentially the same under oxic and anoxic conditions, and net CH 4 consumption under oxic conditions was barely affected by short-term exposure to anoxic conditions. Therefore, methanogens were particularly sensitive to aeration. Net CH 4 production in whole peat increased within hours of adding either acetate, glucose, or ethanol, substrates that methanogens can convert directly or indirectly into CH 4 , indicating that availability of these substrate might limit net CH 4 production in situ. In longer incubations of 30 days, only ethanol addition stimulated a large increase in net CH 4 production, suggesting growth in the population of methanogens when ethanol was available. We fractionated peat into size fractions and the largest sized fraction (> 1.19 mm), composed mostly of roots, showed the greatest net CH 4 production, although net CH 4 production in smaller fractions showed the largest response to ethanol addition. The circumstantial evidence presented here, that ethanol coming from plant roots supports net CH 4 production in forested sites, merits more research.     

Why one species in New Zealand,Pugetia delicatissima (Kallymeniaceae,Rhodophyta), should become two new genera,Judithia gen. nov. and Wendya gen. nov.

Blade-forming red algae occur worldwide and, prior to DNA sequencing, had been notoriously difficult to identify and classify, especially when lacking critical reproductive features. This, coupled in New Zealand with many longstanding assumptions that taxa were identical to non-New Zealand species or genera, resulted in many misapplied names. Pugetia delicatissima R.E. Norris, an endemic New Zealand blade-forming species of the family Kallymeniaceae, is actually comprised of one existing and one new species belonging to two distinct genera, as established by our phylogenetic analyses of DNA sequences from the rbcL gene. Analyses of combined rbcL and LSU genes showed that neither is closely related to the generitype of Pugetia, the northern-eastern Pacific, P. fragilissima Kylin. We propose the names Judithia and Wendya for these two newly revealed genera. In addition to diagnostic rbcL and LSU sequences, Judithia is morphologically and anatomically characterized by rounded to oblong blades that do not taper basally at the stipe, loosely aggregated surface cortical cells and cystocarps lacking both a pericarp and an ostiole, all features observed in the holotype of P. delicatissima. Wendya, in contrast, is characterized by blades that taper both apically and basally, compactly arranged surface cortical cells and cystocarps that have both a pericarp and a distinct ostiole. The two genera also are distinguished from one other, as well as from Pugetia by features of pre- and post-fertilization development, including the number of subsidiary cells produced on carpogonial and auxiliary branch systems, whether subsidiary cells in the carpogonial branch system fuse with the supporting cell or not, and the site of origin of gonimoblast cells. Although small in area, New Zealand hosts ten of the 27 currently recognized genera in the Kallymeniaceae and is the southern-hemisphere region of greatest generic diversification in this family.     

Evolutionary relationships among the Pulmonate land snails and slugs (Pulmonata, Stylommatophora)

We have incorporated an additional 56 species of land snails and slugs in our ribosomal (r) RNA molecular phylogeny. The new taxa include representatives of several important groups. The molecular tree now includes 160 species of stylommatophoran land snails and slugs in 144 genera in 61 families. In the rDNA tree, the Stylommatophora are principally divided into an 'achatinoid' and a 'non-achatinoid' clade. Within these clades, several major land snail groups, including the Orthurethra, Elasmognatha, Limacoidea, and Helicoidea, are supported. Overall, the rDNA molecular phylogeny has remained stable following the incorporation of the additional taxa, with these additions having little impact on the major evolutionary patterns in the tree. Taxonomic coverage of the Orthurethra, Orthalicidae, Camaenidae, and Bradybaenidae is increased significantly. The camaenids and bradybaenids form a complex, and both appear to be paraphyletic. Several families of uncertain affinity, such as the Sagdidae and Thyrophorellidae, are included for the first time. The Sagdidae are shown to belong to the Helicoidea, and the Thyrophorellidae to the Achatinoidea.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 593–610.     

Linking Belowground Carbon Allocation to Anaerobic CH4 and CO2 Production in a Forested Peatland,New York State

Heterotrophic soil microorganisms rely on carbon (C) allocated belowground in plant production, but belowground C allocation (BCA) by plants is a poorly quantified part of ecosystem C cycling, especially, in peat soil. We applied a C balance approach to quantify BCA in a mixed conifer-red maple (Acer rubrum) forest on deep peat soil. Direct measurements of CH₄ and CO₂ fluxes across the soil surface (soil respiration), production of fine and small plant roots, and aboveground litterfall were used to estimate respiration by roots, by mycorrhizae and by free-living soil microorganisms. Measurements occurred in two consecutive years. Soil respiration rates averaged 1.2 bm μmol m^{? 2} s^{? 1} for CO₂ and 0.58 nmol m^{? 2} s^{? 1} for CH₄ (371 to 403 g C m^{? 2} year^{? 1}). Carbon in aboveground litter (144 g C m^{? 2} year^{? 1}) was 84% greater than C in root production (78 g C m^{? 2} year^{? 1}). Complementary in vitro assays located high rates of anaerobic microbial activity, including methanogenesis, in a dense layer of roots overlying the peat soil and in large-sized fragments within the peat matrix. Large-sized fragments were decomposing roots and aboveground leaf and twig litter, indicating that relatively fresh plant production supported most of the anaerobic microbial activity. Respiration by free-living soil microorganisms in deep peat accounted for, at most, 29 to 38 g C m^{? 2} year^{? 1}. These data emphasize the close coupling between plant production, ecosystem-level C cycling and soil microbial ecology, which BCA can help reveal.     

Two New and Two Recharacterized Species from a Radiation of Pristionchus (Nematoda: Diplogastridae) in Europe

Two new species of Pristionchus, P. lucani n. sp. and P. bulgaricus n. sp., are described from France and Bulgaria, respectively. Additionally, new morphological and morphometric data are provided for two previously described species from Europe, P. brevicauda (Kotlán, 1928) Paramonov, 1952 and P. clavus (von Linstow, 1901) Sudhaus and Fürst von Lieven, 2003. A phylogeny including these four species was inferred from a dataset including 26 ribosomal protein-coding genes, sequences of which are original for P. bulgaricus n. sp. and P. clavus. Relationships support a radiation of all sequenced European Pristionchus species from a single, gonochoristic common ancestor, and current knowledge of species ranges supports “western” and “eastern” clades. Similar diagnostic morphologies reflect the close relationships among the new and recharacterized species, especially P. bulgaricus n. sp., P. brevicauda, and P. clavus, although mating tests as well as genetic and phylogenetic separation support their identities as unique species. Our results show that Pristionchus species in Europe are more diverse than typological characters suggest, and thus biological and molecular profiling will be essential for future delimitation of Pristionchus species from the region.     

粤北森林群落优势种群的频度与年龄结构

为探究广东北部山区森林保护现状与发展规律,利用植被样方调查法和数量分析法,研究了粤北18个森林群落乔木层优势种群的频度和高频度（〉60%）种群的年龄结构。结果显示,1265个频度值按Raunkiaer的5个频度等级分析,A级（物种出现概率1%～20%）占78.38%,B级（21%～40%）占15.38%,C级（41%～60%）占2.91%,D级（61%～80%）占1.87%,E级（81%～100%）占1.46%;频度规律为A〉B〉C〉D〉E。在16个频度〉60%（D级和E级）的优势种群的年龄结构中,衰退种群有枫香（Liquidambar formosana）、杉木（Cunning-hamia lanceolata）、小红栲（Castanopsis carlesii）、马尾松（Pinus massoniana）、拟赤杨（Alniphyllum fortunei）、黄樟（Cinnamomum porrectum）、青栲（Castanopsis lamontii）和酸枣（Choerospondias axillarie）;属于增长种群的有红锥（Castanopsis hystrix）、黧蒴（C.fissa）和罗浮栲（C.fabric）;趋于稳定种群的有甜锥（Castanopsis eyrei）、木荷（Schima superba）、红楠（Machilus thunbergii）、罗浮柿（Diospyros morrisiana）和深山含笑（Michelia maudiae）。粤北森林经较长期的群落演替和自然保护,目前针叶树种群及落叶阔叶树种群的衰退,为地带性植被常绿阔叶林及其优势种群的发展奠定了基础。研究结果为粤北自然保护区的建设和可持续发展提供了参考。     

A Novel Alveolate in Bivalves with Chemosynthetic Bacteria Inhabiting Deep‐Sea Methane Seeps

It has recently been unveiled that a wide variety of microbial eukaryotes (protists) occur in chemosynthetic ecosystems, such as hydrothermal vents and methane seeps. However, there is little knowledge regarding protists associated with endemic animals inhabiting these environments. In the present study, utilizing PCR techniques, we detected fragments of the small subunit ribosomal RNA gene (SSU rRNA gene) from a particular protist from gill tissues of a significant fraction of the vesicomyid clams Calyptogena soyoae and C. okutanii complex and of the mussel Bathymodiolus platifrons and B. japonicus, all of which harbor chemosynthetic endosymbiont bacteria and dominate methane seeps in Sagami Bay, Japan. Based on the phylogeny of SSU rRNA gene, the organism in question was shown to belong to Alveolata. It is noteworthy that this protist did not affiliate with any known alveolate group, although being deeply branched within the lineage of Syndiniales, for which the monophyly was constantly recovered, but not robustly supported. In addition, the protist detected using PCR followed by sequencing was localized within gill epithelial cells of B. platifrons with whole‐mount fluorescence in situ hybridization. This protist may be an endoparasite or an endocommensal of Calyptogena spp. and Bathymodiolus spp., and possibly have physiological and ecological impacts on these bivalves.     

Microbial Communities Promoting Mn(II) Oxidation in Ashumet Pond,a Historically Polluted Freshwater Pond Undergoing Remediation

An extensive culture-dependent and -independent study was conducted to identify microorganisms contributing to the biogeochemical cycling of manganese (Mn) in Ashumet Pond, a freshwater pond in Massachusetts currently undergoing remediation. A variety of bacteria (including Gamma-, Beta-, and Alpha-proteobacteria, Firmicutes, and Bacteroides) and Ascoymete fungi were isolated from the pond that promote Mn(II) oxidation and subsequent formation of Mn(III/IV) oxide minerals. Targeted-amplicon pyrosequencing of the bacterial and fungal communities associated with Mn oxide-encrusted samples show a highly diverse microbial community, of which the cultured phylotypes represent a minor proportion. This suggests a larger community, not identified through culturing, contributes to Mn oxide formation within the Pond.     

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: Accelerated sequence evolution,altered promoter structure,and tRNA pseudogenes

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA^Ile and tRNA^Ala present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA^Val gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.     

Lobophora (Dictyotales) Species Richness,Ecology and Biogeography Across the North-Eastern Atlantic Archipelagos and Description of Two New Species1

The brown alga Lobophora (Dictyotales, Phaeophyceae) is an important macroalga in the North-eastern Atlantic archipelagos (i.e., Macaronesia). Notably in the Canaries it can dominate benthic assemblages. While the genus has been the subject of several ecological studies in the Canaries, no study has yet been conducted to assess species-level diversity of Lobophora in Macaronesia. We reassessed the diversity of Lobophora in Macaronesia, reporting the presence of seven species (L. caboverdeana sp. nov., L. canariensis, L. dagamae sp. nov., L. delicata, L. dispersa, L. littlerorum, and L. schneideri). Lobophora spp. from Macaronesia are morphologically and ecologically distinguishable. In the Canaries, L. schneideri dominates the photophilic assemblages from the intertidal to 20-30 m depth. Lobophora dagamae sp. nov. grows in less illuminated shallow habitats, and replaces L. schneideri from 30 to ~80 m. Lobophora canariensis also has a wide vertical distribution, from the intertidal to deep waters, while L. delicata, L. dispersa and L. littlerorum grow in shallow waters. The dominance of species with an upright habit versus prostrate or crustose species may be mediated by the pressure of herbivores. Four species have an amphi-Atlantic distribution: L. littlerorum, L. canariensis, L. delicata, and L. schneideri. Lobophora schneideri and L. delicata are furthermore distributed in the Mediterranean Sea. By sampling a pivotal region in the Atlantic, this study significantly improves our knowledge of Lobophora biogeography in the Atlantic Ocean. Macaronesia constitutes a species–poor region for Lobophora where no diversification events occurred, and a region of overlap between the Greater Caribbean and the Indo-Pacific.     

DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, ‘living fossils’ from the Triassic

The speciation history of Anaspides tasmaniae (Crustacea: Malacostraca) and its close relatives (family Anaspididae) was studied by phylogenetic and molecular clock analyses of mitochondrial DNA sequences. The phylogenetic analyses revealed that the Anaspides morphotype conceals at least three cryptic species belonging to different parts of its range. The occurrence of multiple cryptic phylogenetic species within one morphological type shows that substantial genetic evolution has occurred independently of morphological evolution. Molecular clock dating of the speciation events that generated both the cryptic and the morphological species of Anaspididae indicated continuous speciation within this group since the Palaeocene ~55 million years ago. This relatively constant rate of recent morphological and cryptic speciation within the Anaspididae suggests that the speciation rate in this group does not correlate with its low extinction rate or morphological conservatism.     

High species richness and genetic diversity of the genus Caloglossa (Delesseriaceae,Rhodophyta) in New Ireland,Papua New Guinea

Distribution patterns and genetic diversity of Caloglossa species have been studied in various regions but are still poorly understood around the tropical western Pacific where many marine organisms show high species richness. We explored the diversity of Caloglossa species in New Ireland, Papua New Guinea using morphological and genetic analyses. Seven species of Caloglossa (C. adhaerens, C. leprieurii, C. ogasawaraensis, C. bengalensis, C. postiae, C. saigonensis and C. vieillardii) were collected from eight sites; the latter four species are new records in Papua New Guinea. All specimens collected were cultured to compare their morphology under the same culture condition. Reproductive structures of gametophytes and/or sporophytes were described for the first time in some species from these collections. In C. leprieurii, gall‐like structure appeared in most gametophyte strains but not in tetrasporophytes. Such galls were produced from wing cells, and spermatangia and/or procarps were formed on many galls. The LSU rDNA and rbcL analyses revealed high intraspecific diversity in many species although the number of samples was limited and the sampling sites were within 200 km. We revealed high species richness and intraspecific genetic variation in Papua New Guinea, suggesting a hot spot for the diversity of Caloglossa.     

Large Amounts of Genetic Divergence among Italian Species of the Genus Orchesella (Insecta, Collembola) and the Relationships of Two New Species

The phylogenetic position of two putative new species of the collembolan genus Orchesella was investigated by comparison with four other Italian species of the genus using a fragment of the mitochondrial gene encoding for subunit I of cytochrome c oxidase (COI). The gene showed the well-known A + T bias, typical of insect mitochondrial DNA, although A + T content was not as high as that observed in species belonging to more derived insect orders. The large number of variable sites in 3rd codon positions (85.2% variable) suggested that these sites contain significant homoplasy due to multiple hits. Despite the lack of morphological differentiation, the COI portion examined shows remarkable levels of genetic divergence between the putative species and their closest relatives. Phylogenetic analysis suggests that one of the putative new species is related to O. villosa, whereas the other is included in a clade with O. cincta and O. ranzii. The species O. chiantica appears to be related to O. villosa, agreeing with previous allozyme data.     

Genetic diversity,admixture, and hatchery influence in Brook Trout (Salvelinus fontinalis) throughout western New York State

Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non‐native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation‐decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F_ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% (q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.     

Environmental effects on biofilm bacterial communities: a comparison of natural and anthropogenic factors in New Zealand streams

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