Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog

The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (>or=95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3x10(7) and 1.1x10(7) cells g-1 peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.     

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

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.Subject terms: Microbial ecology, Metagenomics, Soil microbiology, Biogeochemistry, Microbial ecology     

Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog

Sites in the West Siberian peat bog 'Bakchar' were acidic (pH 4.2-4.8), low in nutrients, and emitted CH4 at rates of 0.2-1.5 mmol m(-2) h(-1). The vertical profile of delta13CH4 and delta13CO2 dissolved in the porewater indicated increasing isotope fractionation and thus increasing contribution of H2/CO2-dependent methanogenesis with depth. The anaerobic microbial community at 30-50 cm below the water table produced CH4 with optimum activity at 20-25 degrees C and pH 5.0-5.5 respectively. Inhibition of methanogenesis with 2-bromo-ethane sulphonate showed that acetate, phenyl acetate, phenyl propionate and caproate were important intermediates in the degradation pathway of organic matter to CH4. Further degradation of these intermediates indicated that 62-72% of the CH4 was ultimately derived from acetate, the remainder from H2/CO2. Turnover times of [2-14C]acetate were on the order of 2 days (15, 25 degrees C) and accounted for 60-65% of total CH4 production. Conversion of 14CO2 to 14CH4 accounted for 35-43% of total CH4 production. These results showed that acetoclastic and hydrogenotrophic methanogenesis operated closely at a ratio of approximately 2 : 1 irrespective of the incubation temperature (4, 15 and 25 degrees C). The composition of the archaeal community was determined in the peat samples by terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of amplified SSU rRNA gene fragments, and showed that members of Methanomicrobiaceae, Methanosarcinaceae and Rice cluster II (RC-II) were present. Other, presumably non-methanogenic archaeal clusters (group III, RC-IV, RC-V, RC-VI) were also detected. Fluorescent in situ hybridization (FISH) showed that the number of Bacteria decreased (from 24 x 10(7) to 4 x 10(7) cells per gram peat) with depth (from 5 to 55 cm below the water table), whereas the numbers of Archaea slightly increased (from 1 x 10(7) to 2 x 10(7) cells per gram peat). Methanosarcina spp. accounted for about half of the archaeal cells. Our results show that both hydrogenotrophic and acetoclastic methanogenesis are an integral part of the CH4-producing pathway in acidic peat and were represented by appropriate methanogenic populations.     

Bacterial degradation of styrene in waste gases using a peat filter

A biofiltration process was developed for styrene-containing off-gases using peat as filter material. The average styrene reduction ratio after 190 days of operation was 70% (max. 98%) and the mean styrene elimination capacity was 12 g m⁻³ h⁻¹ (max. 30 g m⁻³ h⁻¹). Efficient styrene degradation required addition of nutrients to the peat, adjustment of the pH to a neutral level and efficient control of the humidity. Maintenance of the water balance was easier in a down-flow than in an up-flow process, the former consequently resulting in much better filtration efficiency. The optimum operation temperature was around 23 °C, but the styrene removal was still satisfactory at 12 °C. Seven different bacterial isolates belonging to the genera Tsukamurella, Pseudomonas, Sphingomonas, Xanthomonas and an unidentified genus in the γ group of the Proteobacteria isolated from the microflora of active peat filter material were capable of styrene degradation. The isolates differed in their capacity to decompose styrene to carbon dioxide and assimilate it to biomass. No toxic intermediate degradation products of styrene were detected in the filter outlet gas or in growing cultures of isolated bacteria. The use of these isolates in industrial biofilters is beneficial at low styrene concentrations and is safe from both the environmental and public health points of view. Received: 30 May 1997 / Received revision: 22 August 1997 / Accepted: 25 August 1997     

Influence of environmental factors on 2,4-dichlorophenoxyacetic acid degradation by Pseudomonas cepacia isolated from peat

A Pseudomonas cepacia, designated strain BRI6001, was isolated from peat by enrichment culture using 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. BRI6001 grew at up to 13 mM 2,4-D, and degraded 1 mM 2,4-D at an average starting population density as low as 1.5 cells/ml. Degradation was optimal at acidic pH, but could also be inhibited at low pH, associated with chloride release from the substrate, and the limited buffering capacity of the growth medium. The only metabolite detected during growth on 2,4-D was 2,4-dichlorophenol (2,4-DCP), and degradation of the aromatic nucleus was by intradiol cleavage. Growth lag times prior to the on-set of degradation, and the total time required for degradation, were linearly related to the starting population density and the initial 2,4-D concentration. BRI6001, grown on 2,4-D, oxidized a variety of structurally similar chlorinated aromatic compounds accompanied by stoichiometric chloride release.     

Denitrification triggered by nitrogen addition in Sphagnum magellanicum peat

Ombrotrophic (rain-fed) Sphagnum-mires do not significantly contribute to gaseous nitrogen (N) emissions to the atmosphere. However, increasing levels of N deposition reduce Sphagnum growth and moss cover. As a consequence, higher amounts of mineral N reach the underlying peat beneath the moss layer. The aim of our work was to determine the effects of supplementary N inputs to peat beneath Sphagnum magellanicum carpets. Peat cores were incubated in controlled laboratory conditions of temperature and humidity, and the impact of increasing N inputs was evaluated on denitrification rates, basal respiration and methane emissions. Rates of denitrification were quickly stimulated by addition of 1?g?N?m^?2 but rates were not significantly elevated in the short-term (9?days) by further additions of up to 10?g?N?m^?2. Over a longer term period (up to 45?days), denitrification rates followed an exponential (10?g?N?m^?2 addition) or a gamma (1?g?N?m^?2) function. Findings from this study support the hypothesis that mineral-N addition in atmospheric deposition will have a negative effect on peat biogeochemistry, by modifying its N sink capacity via denitrification leading to a potential increase in N₂O emissions.     

Sphagnum establishment on bare peat: The importance of climatic variability and Sphagnum species richness

Question: What is the relative ability of four species of Sphagnum (S. fuscum, S. rubellum, S. magellanicum and S. angustifolium) to establish on bare peat substratum in the field when re‐introduced as single or multi‐species re‐introductions and in relation to interannual variations in climate? Location: Continental southeastern Canada. Methods: Diaspores (fragments) of four Sphagnum species alone or in combination were re‐introduced onto residual peat surfaces and were monitored to follow the development of the moss carpet over four growing seasons. In order to compare results under a variety of climatic conditions, this whole experimental setting was repeated four times (trials), with a four‐year follow‐up for each trial. Conclusions: The establishment rate of the moss carpet varied among years, in response to climatic variations between growing seasons. The relative success of different moss species and combinations of species, however, did not vary within or between trials. Thus, the species and combinations of species resulting in the highest short‐term or long‐term establishment rates remained the same for all trials, independent of the climatic conditions at the time of re‐introduction. Our results showed no link between the number of species in the diaspore mixture and successful establishment of the moss carpet. Yet successful regeneration was clearly influenced by the identity of species chosen for re‐introduction. S. fuscum, alone or in combination, was the species found to lead to the most extensive development of the moss carpet under the current test conditions.     

Factors controlling pelagic populations of ciliates and heliozoans-- late summer investigations in an acidic lake before and after liming

Ciliates and heliozoans were studied in a small oligotrophicSwedish lake with the objective of investigating what controlledthe community structure and population dynamics. Enclosure experimentswere performed with five levels of inorganic nutrient concentrationsand the presence or absence of crustacean zooplankton. The experimentswere performed during the summers immediately preceding andfollowing liming of the lake. The responses of protozooplanktonto these manipulations were investigated and compared with theresponses of bacterioplankton, phytoplankton and metazooplankton.In contrast to most studies on protozoan zooplankton, ciliateswere determined to the lowest taxon possible, and biomassesand abundances were calculated for the different taxa. The protozooplanktonbiomass of the lake, expressed as summer average, did not changebetween the years. However, the community composition changedfrom smaller to larger species as the small prostomatid ciliatesUrotricha and Balanion were largely replaced by oligotrichsof the genera Strombidium and Strobilidium. The experimentssuggested that the protozooplankton community in the lake wascontrolled by metazooplankton in the acidic environment, whilefood limitation was the most important controlling factor afterliming. Before liming, Urotricha and Balanion were unaffectedby nutrient additions as well as by metazooplankton, while otherciliates and Heliozoa showed a significantly negative responseto metazooplankton. After liming, Urotricha and Balanion showeda significant positive response to nutrient addition as wellas to bacterioplankton biomass. A possible explanation for thisresponse in these algivore genera is that the response was indirectand mediated through small chrysoflagellates.     

泥炭地特征性环境因子促进泥炭藓持久孢子库的形成

研究泥炭地特征性环境因子——淹水、少氧和化感物质对泥炭藓孢子持久性的影响, 可深入理解泥炭地泥炭藓持久孢子库的形成机制, 为退化泥炭地泥炭藓地被恢复研究提供参考。该研究以藓丘种和丘间种两种泥炭藓的孢子为试验材料, 通过室内模拟控制实验的方法, 研究泥炭藓孢子在空气、超纯水、泥炭地地表水和泥炭藓沥出液中, 及3种速率充气下, 孢子萌发力持久性的变化。经充气处理后, 泥炭藓孢子持久性显著低于不充气处理。不充气时, 泥炭藓孢子在含有化感物质的泥炭地地表水和泥炭藓沥出液中保存, 持久性显著高于在超纯水中保存。通径分析结果显示, 溶解氧是影响泥炭地泥炭藓孢子持久性的主要因子和限制因子, 养分元素氮(TN)和磷(TP)的浓度为孢子持久性的负作用因子。研究结果表明, 泥炭藓孢子散布于苔藓地被基质或淹水的丘间生境中, 比暴露于空气或在无化感物质的水中, 能更好地维持萌发力。泥炭地中, 泥炭藓孢子和其他植物的繁殖体的超长寿命可能归因于少氧、养分贫乏和丰富的化感物质等泥炭地特征性环境因子。     

Recombination and introgression of nuclear and chloroplast genomes between the peat mosses, Sphagnum capillifolium and Sphagnum quinquefarium

Haploid hybrid gametophytes are often present at low frequencies in sympatric populations of Sphagnum capillifolium and Sphagnum quinquefarium. We used intersimple sequence repeat (ISSR) markers and polymerase chain reaction-restriction fragment length polymorphism of the trnL(UAA) intron of the chloroplast genome to reveal the nuclear and chloroplast composition of mature hybrid gametophytes from natural populations and of gametophytes derived from spores of hybrid sporophytes collected in nature. Asymmetrical nuclear inheritance was found in the progeny of the hybrid sporophytes, indicating that only spores with a low level of recombination of parental genomes were viable. A similarly skewed nuclear composition was found among the naturally occurring hybrid gametophytes. All hybrid genomes contained a larger proportion of S. capillifolium ISSR markers, combined with only two to five S. quinquefarium markers together with a chloroplast haplotype derived from S. quinquefarium. In this way, a pattern resembling introgression is created within a single generation. Some individuals possessed nuclear genomes typical for S. capillifolium in combination with the chloroplast haplotype of S. quinquefarium, possibly indicating backcrossing. Our results indicate that hybridization between S. capillifolium and S. quinquefarium is relatively common, but the resistance of large parts of the genome against heterospecific genes maintains the genetic distinctness of the species. Further evolutionary and phylogenetic consequences of restricted interspecific gene exchange are discussed.     

Rockin' in rhythm,growth dynamics of the peat moss Sphagnum

The genus Sphagnum is an essential component in the formation and maintenance of high latitude peatlands, bogs and mires. The species grows in dense, extended mats of agglomerated shoots that allow it to retain water necessary for its growth. These mats are partly responsible for maintaining the right conditions for other species in these wetlands to thrive. In this issue of Physiologia Plantarum, Mironov et al. (2020) monitored the growth of Sphagnum riparium for a period of 4 years and revealed three distinct growth rhythms: a seasonal temperature dependent, a circalunar and a third one, synchronized with the circalunar. This synchronised nature of Sphagnum growth could contribute to its position as a key species in the maintenance of peatlands.     

High abundance of planctomycetes in anoxic layers of a Sphagnum peat bog

The depth distribution of planctomycete abundance has been examined in six different sites of the Sphagnum peat bog Bakchar, Tomsk oblast, Russia. In situ hybridization of peat with the fluorescently labeled oligonucleotide probes PLA46 and PLA886, reported to be group-specific for representatives of the phylum Planctomycetes, revealed two distinct population maxima of these bacteria in all of the profiles examined. The first population maximum was detected in the uppermost, oxic layer of the bog profile, while the second maximum was located at a depth of 30 cm below the water table level. The population sizes of planctomycetes in the uppermost layer and at a depth of 30 cm were of the same order of magnitude and comprised 0.5–1.5 × 10⁷ and 0.4?0.7 × 10⁷ cells per g^?1 of wet peat, respectively. Only 25–30% of the total number of planctomycete cells in the anoxic layer could be detected if the probe PLA886, whose target specificity is restricted to taxonomically characterized aerobic planctomycetes of the genera Gemmata, Planctomyces, Pirellula, and Isosphaera, was used alone. Other planctomycete cells in this layer were detected only with the probe PLA46, which possesses a much wider scope. This suggests the affiliation of these organisms with a yet undescribed phylogenetic subgroup within the Planctomycetes.     

High abundance of planctomycetes in anoxic layers of a Sphagnum peat bog

The depth distribution of planctomycete abundance has been examined in six different sites of the Sphagnum peat bog in Bakchar, Tomsk oblast, Russia. In situ hybridization of peat with the fluorescently labeled oligonucleotide probes PLA46 and PLA886, reported to be group-specific for representatives of the phylum Planctomycetes, revealed two distinct population maxima of these bacteria in all of the profiles examined. The first population maximum was detected in the uppermost, oxic layer of the bog profile, while the second maximum was located at a depth of 30 cm below the water table level. The population sizes of planctomycetes in the uppermost layer and at a depth of 30 cm were of the same order of magnitude and comprised 0.5-1.5 x 10(7) and 0.4-0.7 x 10(7) cells per g of wet peat, respectively. Only 25-30% of the total number of planctomycete cells in the anoxic layer could be detected if the probe PLA886, whose target specificity is restricted to taxonomically characterized aerobic planctomycetes of the genera Gemmata, Planctomyces, Pirellula, and Isosphaera, was used alone. Other planctomycete cells in this layer were detected only with the probe PLA46, which possesses a much wider scope. This suggests the affiliation of these organisms with a yet undescribed phylogenetic subgroup within the Planctomycetes.     

鄂西南亚高山不同覆被类型泥炭藓沼泽湿地甲烷排放特征及其环境影响因子

沼泽湿地是大气甲烷(CH₄)的重要来源, 但有关亚热带亚高山沼泽湿地CH₄排放的研究却鲜有报道, 特别是对不同覆被类型泥炭藓沼泽湿地CH₄排放量的精确估算及其与环境因子的关系尚不清楚。该研究选择鄂西南亚高山泥炭藓沼泽湿地为研究区域, 于2018年11月-2019年10月间, 使用静态箱-气相色谱仪法原位测定3种覆被类型泥炭藓沼泽湿地CH₄通量, 同步记录大气和地下5 cm土壤的温度以及地下水位变化。结果表明: (1)光照下, 裸露地(B)、泥炭藓(Sphagnum paluster)(S)、金发藓(Polytrichum commune)(P) 3种覆被类型泥炭藓沼泽湿地CH₄-C通量全年变化范围分别为: 0.012-1.372、0.022-1.474、0.027-3.385 mg·m^-2·h^-1; 遮光处理下, B、S、P 3种覆被类型泥炭藓沼泽湿地CH₄-C通量的全年变化范围分别为: 0.012-1.372、0.009-1.839、0.017-2.484 mg·m^-2·h^-1, 均为CH₄排放源。同时, 光照条件下不同覆被泥炭藓沼泽湿地CH₄排放量略大于黑暗条件, 但差异不明显。(2)不同覆被类型泥炭藓沼泽湿地CH₄排放存在明显的季节变化规律, 即: 夏季>秋季>春季>冬季, 其中夏季CH₄排放量显著大于其他季节, 占全年的57%-84%。该研究发现泥炭藓沼泽湿地CH₄通量均与气温和地下5 cm土壤温度极显著相关, 且CH₄排放量随温度升高呈指数增加, 表明温度是影响泥炭藓沼泽湿地CH₄排放时间变化的主要环境因子。(3) 3种覆被类型泥炭藓沼泽湿地的年平均和年累计CH₄排放量均依次为: P > S > B, P显著大于B。该研究发现植被类型与泥炭藓沼泽湿地CH₄排放量存在显著相关性, 表明覆被类型是影响泥炭藓沼泽湿地CH₄排放量空间变异的主要因子。(4) 3种覆被类型泥炭藓沼泽湿地CH₄排放量均与地下水位变化不相关。该研究进一步丰富了泥炭藓沼泽湿地CH₄排放规律, 同时也为区域碳循环提供了详实的基础数据。     

Sphagnum distribution patterns along environmental gradients in Bulgaria

Abstract

The distribution patterns of 18 Sphagnum species along base-richness and altitudinal gradients were studied in Bulgarian treeless wetlands which are noteworthy because of the edge-of-range occurrence of many mire species including Sphagnum. Of 483 spring and mire sites studied, 202 samples contained some Sphagnum species. The most common species were S. subsecundum (n=85), S. platyphyllum (46), S. contortum (41), S. teres (40) and S. capillifolium (26). The significance of Sphagnum responses to environmental gradients was tested by comparing generalized additive models against the null model. Many Sphagnum species displayed a significant response to the altitudinal gradient. Several species were clearly linked to low or to high altitudes, but the realized niche of other species was wide with respect to altitude. Most species significantly responded to water pH, both above and below the timberline. The same result was obtained for water conductivity below the timberline, whereas only a few species had a significant response to conductivity above the timberline. The highest water conductivity under which Sphagnum species occurred was 280 μS cm^?1. Sphagnum contortum was the species occupying the mires with the highest mineral content. On the contrary, Sphagnum warnstorfii, one of the most calcitolerant species in many regions of Europe, often occurred in extremely mineral-poor mires above the timberline. Some other Sphagnum species growing in mineral-rich mires below the timberline, also inhabited extremely mineral-poor mires above the timberline. This could be explained by adaptation to local conditions during long-term isolation on mineral-poor bedrock or by changed competition pressure.     

Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation methods

By means of fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes (FISH), it has been shown that members of the phylum Planctomycetes represent a numerically significant bacterial group in boreal Sphagnum peat bogs. The population size of planctomycetes in oxic layers of the peat bog profile was in the range of 0.4-2.0 x 10(7) cells per g of wet peat, comprising 4 to 13% of the total bacterial cell number. A novel effective approach that combined a traditional cultivation technique with FISH-mediated monitoring of the target organism during the isolation procedure has been developed for the isolation of planctomycetes. Using this approach, we succeeded in isolating several peat-inhabiting planctomycetes in a pure culture. Sequencing of the 16S rRNA genes from two of these isolates, strains A10 and MPL7, showed that they belonged to the planctomycete lineages defined by the genera Gemmata and Planctomyces, respectively. The 16S rRNA gene sequence similarity between strains A10 and MPL7 and the phylogenetically closest organisms, namely, Gemmata obscuriglobus and Planctomyces limnophilus, was only 90%. These results suggest that the indigenous planctomycetes inhabiting Sphagnum peat bogs are so far unknown organisms.