Bog Soils Research Articles

Soil Microbial Community Structure and Its Contribution to Carbon Cycling in the Yalu River Estuary Wetland

Wetland microbial communities play a vital role in ecosystem functioning, particularly in the intricate processes of carbon cycling. This study employed metagenomic sequencing to investigate the diversity, composition, structural differences, carbon cycling functional gene, and microbial species of soil microbial communities in five distinct soil types of the Yalu River estuary wetland, including shoal soil, bog soil, paddy soil, meadow soil, and brown forest soil. We further explored the influence of environmental factors on both the microbial community structure and carbon cycling functional genes. Our results revealed a bacterial-dominated soil microbial community, constituting about 97.6%. Archaea and fungi represented relatively minor fractions, at 1.9% and 0.4%, respectively. While no significant differences were observed in Chao1 indices between bacterial and fungal communities, the Shannon index revealed notable differences. Both Chao1 and Shannon indices exhibited significant variations within the archaeal communities. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae. Thaumarchaeota, Crenarchaeota, and Euryarchaeota formed the major archaeal phyla, while Ascomycota, Mucoromycota, and Basidiomycota were the dominant fungal phyla. Non-metric multidimensional scaling (NMDS) analysis based on Bray-Curtis distance revealed notable differences in the bacterial, archaeal, and fungal community structures across the samples. Redundancy analysis (RDA) identified key environmental factors for the major phyla. Soil pH, soil organic carbon (SOC), electrical conductivity (EC), and total phosphorus (TP) were the main influencing factors for bacteria, while soil TP, EC, total sulfur (TS), and SOC were the primary drivers for archaeal phyla. Soil total nitrogen (TN) and EC were the main influencing factors for fungal phyla. Analysis of key carbon cycling pathway genes utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and clustering heatmap revealed some variations in functional gene composition across different soil types. Mantel test indicated that pH, TN, and SOC were the primary environmental factors influencing microbial functional genes associated with soil carbon cycling. Stratified bar chart analysis further demonstrated that the major contributors to carbon cycling originated from corresponding dominatnt phyla and genera of Proteobacteria, Thaumarchaeota, Actinomycetota, Euryarchaeota, and Bacteroidota. The species and relative abundance of microorganisms associated with carbon cycling pathways varied among the samples. These findings provide a crucial reference for informing the conservation and sustainable management of wetland ecosystems in the Yalu River estuary.

Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation.

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

Diversification of Intensively Used Grassland: Resilience and Good Fodder Quality across Different Soil Types

In Central Europe, grasslands for dairy production are typically characterised by monocultures with high input rates of artificial fertilisers. However, it was suggested that biodiversity could reduce the need for anthropogenic inputs in functionally diversified grassland mixes while maintaining or enhancing yields and fodder quality. To investigate this hypothesis, we developed five consecutively diversified grassland mixes consisting of ryegrass, legumes, a non-leguminous forb, and additional grass species for intensive fodder production, and tested them under regular agricultural conditions in a three-year experiment on sandy soil, marshland, and bog soil at one-hectare per mix and site. All mixtures produced similar high-quality forage in terms of utilisable crude protein content and net energy lactation rate, even under challenging climatic conditions. However, a high abundance of Dactylis glomerata can decrease these values, although factors such as seasonality and rainfall affect them to a greater degree. The seasonal composition changes between the functional groups, such as strong spring growth of grasses and strong summer growth of legumes, show complementarity rather than competition between the groups, resulting in consistent biomass production during the growth period. The results were consistent over the three soil types and provide the basis for further adaptation of mixes and breeding.

Phosphorus Supply to Plants of Vaccinium L. Genus: Proven Patterns and Unexplored Issues

Phosphorus availability is a serious problem for plants growing and grown in acidic soils of bogs, poor in macronutrients. The application of phosphorus fertilizers to such soils is unprofitable because of the physical and chemical properties of these soils, where phosphate is firmly bound to organic and inorganic compounds and becomes inaccessible to plants. Plants of the Vaccinium genus both from natural stands and commercial plantations may suffer from phosphorus deficiency, so they need to have a number of adaptations that allow them to efficiently extract phosphorus. This review addresses the following issues in relation to plants of the Vaccinium genus: sources of phosphorus for plants; the release of phosphate ions from soil components; the transport of phosphate ions into plants; and the importance of mycorrhiza in supplying phosphorus to plants. Thus, we sought to draw researchers’ attention to sources and routes of phosphorus supply of plants of the Vaccinium genus and its unexplored aspects.

Diversity and Biological Activities of Mold Isolated from Bilanko and Ngamakala Peat Bog Soils (Republic of Congo)

Diversity and Biological Activities of Mold Isolated from Bilanko and Ngamakala Peat Bog Soils (Republic of Congo)

Physicochemical and Bacteriological Profile of Bilanko and Ngamakala Peat Bog Soils (Republic of Congo)

Physicochemical and Bacteriological Profile of Bilanko and Ngamakala Peat Bog Soils (Republic of Congo)

Enrichment of mixed methanotrophic cultures producing polyhydroxyalkanoates (PHAs) from various environmental sources

Methanotrophic bacteria can use atmospheric methane (CH4) as a sole carbon source for the growth and production of polyhydroxyalkanoates (PHA). The development of CH4 bioconversion processes relies heavily on the selection of an efficient methanotrophic culture. This research assessed the effect of selected growth conditions, such as nitrogen sources on the enrichment of methanotrophic cultures from various environments for PHA accumulation. Nitrate-based medium favoured the culture growth and selection for PHA-producing methanotrophic cultures with Methylocystis sp. as a major genus and accumulation of up to 27 % polyhydroxybutyrate (PHB) in the biomass. Three PHB-producing cultures: enriched from waste activated sludge (AS), peat bog soil (PB) and landfill biocover soil (LB) were then tested for their ability to produce PHA copolymer at different CH4:O2 ratios. All enriched cultures were able to utilise valeric acid as a cosubstrate for the accumulation of PHA with a 3-hydroxyvaleric (3HV) fraction of 21–41 mol% depending on the inoculum source and CH4 concentration. The process performance of selected cultures was evaluated and compared to the culture of reference strain Methylocystis hirsuta DSM 18500. All mixed cultures irrespective of their inoculum source had similar levels of 3HV fraction in the PHA (38 ± 2 mol%). The highest poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production was observed for AS culture at 10 % CH4 with an accumulation of 27 ± 3 % of dry cell weight (DCW), 3HV fraction of 39 ± 2 mol% and yield of 0.42 ± 0.02 g-PHA/g-substrate.

Sphagnum Litter as the Most Important Genetic Horizon in the Profile of Peat Soils of Boreal Bogs

Sphagnum Litter as the Most Important Genetic Horizon in the Profile of Peat Soils of Boreal Bogs

Sphagnum Litter as the Most Important Genetic Horizon in the Profile of Peat Soils of Boreal Bogs

Peat soils of the taiga zone of West Siberia have historically been relatively poorly studied. In the diagnostics of peat soils, the question of the belonging of the sphagnum litter horizon to the soil profile, as well as the identification of its lower boundary, remains unresolved. In the WRB and Russian Soil Classification, sphagnum litter is considered as a vegetation cover, while in the Soviet classification it is considered as an integral part of the soil profile. The last point of view is also shared by the majority of Russian researchers. Using the material obtained in the study of peat soils in the basin of the river Kazym (subzone of the northern taiga, West Siberia), a comparative characteristic of the sphagnum litter horizon (0–20 cm) and the underlying peat horizon (20–50 cm) was carried out using three parameters: the botanical composition of peat, the degree of peat decomposition, and the color of the soil. All soils are differentiated into the litter horizon and the peat horizon by at least one parameter (5% of the profiles), but in 71% of cases, by three at once. The degree of profile differentiation into two horizons tends to increase in a series of soils formed, respectively, in oligotrophic pine-shrub-sphagnum, oligotrophic complex ridge-hollow, and mesotrophic biogeocenoses. In the overwhelming majority of oligotrophic peat soils, the transition from the litter horizon to the peat horizon is gradual, which does not allow a reproducible assessment of the boundary position in the soil profile. It is proposed to establish a fixed border of the litter horizon at 20 cm from the surface of the bog, referring it to the surface horizon of peat soil.

Carbon Dioxide Emission from Soils of the Ecotone Zone in the North of Western Siberia

The study area in the north of Western Siberia is located in the southern tundra–taiga ecotone near the southern boundary of discontinuous permafrost zone. Three contrasting ecosystems—pine forests with Albic Podzols; palsa with Histic Oxyaquic Turbic Cryosols, and bogs with Fibric Histosols—predominate in this area. The objectives of the study included evaluation of the CO2 emission from soils in the growing seasons of 2019–2022 and analysis of the factors controlling spatial and interannual variability of the emission. The study included analysis of the soil respiration (static closed chamber method) data and soil hydrothermal parameters in August for four years. In the absence of definite trends in climatic parameters over the past 10 years, a gradual increase in the soil temperature in all ecosystems and an increase in the depth of summer thawing in palsa were observed. These changes were not accompanied by significant changes in the CO2 emission. Its averaged values varied from 485 to 540 mg CO2/(m2 h) in forest ecosystems and from 150 to 255 mg CO2/(m2 h) in the palsa–bog complex with high coefficients of spatial variability. High CO2 emission in forest ecosystems is determined by a favorable hydrothermal regime, high root biomass, and good water-physical properties. Part of the CO2 produced by palsa soils is transported with suprapermafrost water flows toward the adjacent bog and is released from the surface of bog soils. Soil temperature interrelated with seasonal thawing depth proved to be a significant predictor of the spatial variability of CO2 emission from the soils of the palsa–bog complex.

CO<sub>2</sub> Emission by Soils of the Ecotone Zone in the North of Western Siberia

The study area in the North of Western Siberia is located at the southern limit of the distribution of surficial permafrost in the ecotone zone on the border of taiga and southern tundra. Area is characterized by the contrasting landscapes: pine forests with Albic Podzol; palsa with Histic Oxyaquic Turbic Cryosol and bog ecosystems with Fibric Histosol. The objectives of the study included evaluation the values of CO2 emission (SR) by soils of key landscapes in the growing seasons of 2019–2022, and evaluation the factors of spatial variability of this indicator and its interannual variability. The study included analysis of the RS database (static closed chamber method) and soil hydrothermal parameters for four years in August. In the absence of trends in changing climatic parameters over the past 10 years, a gradual increase in soil temperature in all landscapes and an increase in the depth of thawing in palsa were observed. These changes were not accompanied by significant changes in the SR value. It averaged from 485 to 540 mgCO2/(m2 h) in forest ecosystems, from 150 to 255 mgCO2/(m2 h) in the peat-bog complex with high coefficients of spatial variability. High values of SR in forest ecosystems are determined by a favorable hydrothermal regime, high reserves of root biomass, and good water-physical properties. Part of the CO2 produced by palsa soils is transported by supra-permafrost waters and released from the surface of bog soils. Soil temperature, regulated by seasonal thawing, was a significant predictor of the spatial variability of SR on the soils of the palsa-bog complex.

Permafrost Effect on the Spatial Distribution of CO2 Emission in the North of Western Siberia (Russia)

The landscapes in the discontinuous permafrost area of Western Siberia are unique objects for assessing the direct and indirect impact of permafrost on greenhouse gas fluxes. The aim of this study was to identify the influence of permafrost on the CO2 emission at the landscape and local levels. The CO2 emission from the soil surface with the removed vegetation cover was measured by the closed chamber method, with simultaneous measurements of topsoil temperature and moisture and thawing depth in forest, palsa, and bog ecosystems in August 2022. The CO2 emissions from the soils of the forest ecosystems averaged 485 mg CO2 m−2 h−1 and was 3–3.5 times higher than those from the peat soils of the palsa mound and adjacent bog (on average, 150 mg CO2 m−2 h−1). The high CO2 emission in the forest was due to the mild soil temperature regime, high root biomass, and good water–air permeability of soils in the absence of permafrost. A considerable warming of bog soils, and the redistribution of CO2 between the elevated palsa and the bog depression with water flows above the permafrost table, equalized the values of CO2 emissions from the palsa and bog soils. Soil moisture was a significant factor of the spatial variability in the CO2 emission at all levels. The temperature affected the CO2 emission only at the sites with a shallow thawing depth.

Thermal Hazards Evaluation Based on Weight of Evidence Method in the Resource Area of Datong River in Qinghai-Tibetan Plateau

With global warming and increasingly frequent human activities in permafrost regions, it is of great significance to accurately and scientifically evaluate the probability and scope of thermal hazards in permafrost regions. Based on remote sensing image interpretation and field survey, the weight of evidence method (WoEM) was used to comprehensively evaluate the risk of thermal hazards in the source area of the Datong River. There were 10 factors, such as ground ice, mean annual ground temperature, mean annual air temperature, and ground soil type etc., selected in the WoEM. The results showed that the thermal hazard occurrences were closely influenced by ground ice, mean annual ground temperature, ground soil type, etc. The thermal hazards mainly occurred in the unstable permafrost with MAGT of –0.5 to –1.5 °C, accounting for 54.72% of the thermal hazards. The distribution area of thermal hazards in ground ice Level I and II accounts for 66.42%. Thermal hazards mainly occur in the soil types of bog soil and sapropel bog soil, accounting for 41.24% and 29.62% of the total thermal hazards area, respectively. Based on the influence factors and WoEM of thermal hazards occurrence, the probability map of thermal hazards occurrence in the source area was obtained. Additionally, the characteristics of the region with a high probability of thermal hazards occurrence and their causes were also comprehensively analyzed.

Microbial organic matter reduction regulates methane and carbon dioxide production across an ombrotrophic-minerotrophic peatland gradient

Unraveling the mechanistic controls of methane (CH4) cycling in northern peatland ecosystems is crucial for understanding peatland-climate feedbacks. Growing evidence indicates that the microbial reduction of organic matter as a terminal electron acceptor can be a key regulator of CH4 production in peatlands, but the role of microbial organic matter reduction in different peatlands has not been well explored. Using an electron shuttling capacity assay, we investigated the relationship between the microbial reduction of organic matter and anaerobic CH4 and carbon dioxide (CO2) production in peatland soils in three experiments. In the first experiment, we surveyed the importance of microbial organic matter reduction in six soils representing the ombrotrophic-minerotrophic peatland gradient. In the second experiment, we further explored the reduction of solid-phase organic electron acceptors in a minerotrophic fen and compared these results to previously published values from an ombrotrophic bog (the end members of the initial gradient surveyed). Results from these experiments suggest that microbial organic matter reduction suppresses CH4 production, especially in ombrotrophic peat soils, likely helping to explain low CH4 production in bog-like soils. In contrast, the pool of oxidized organic matter was quickly reduced in minerotrophic peat soils which subsequently exhibited higher rates of CH4 production. In the final experiment, we investigated the effect of temperature on microbial organic matter reduction in the same ombrotrophic bog soil, demonstrating that warmer temperatures resulted in both a faster reduction of solid-phase organic matter and an apparent increase in the size of the organic electron acceptor pool that can be reduced by microbes. Future work should explore the drivers of the observed differences in microbial organic matter reduction in different peatland soils to provide a stronger mechanistic explanation for how this process will regulate peatland greenhouse gas dynamics in the face of global change, including increases in temperature.

Soil Based Adsorption Media for Permeable Reactive Barriers to Adsorb Lead (Pb<sup>2+</sup>) & Cadmium (Cd<sup>2+</sup>)

Groundwater contamination is one of the predominant environmental problems in Sri Lanka and it is suspected as one of the unseen factors of the country’s widespread kidney disease. Heavy metals Cadmium (Cd2+) and Lead (Pb2+) are two potentially harmful contaminants found in polluted groundwater samples in Sri Lanka. Permeable reactive barrier (PRB) is an on-site, costeffective and efficient groundwater heavy metal remediation technique. However, the effectiveness of the PRB system is highly dependent on the characteristics of the reactive materials being used. Accordingly, Rendzina soil (Hunugala series), Reddish Brown earth soil (Nonagama series), Reddish brown latosolic soil (Melsiripura series), and Bog Soil (Wagura series) were selected based on the basic soil properties which were found by previous researchers. Sieve analysis, Atterberg limits, and Procter compaction tests were carried out to determine the physical properties of the selected soils. The batch tests were carried out to determine the absorption rate of heavy metals, namely, Lead (Pb2+) and Cadmium (Cd2+), and to assess the effects of pH, contact time, and initial concentration on the adsorption characteristics of the selected reactive materials. The results reveal that the Rendzima soil is the most suitable reactive material out of all the reactive materials tested.

Traces of past bog burning culture in rewetted bog soils (Emsland region, Germany)

Until the beginning of the 20th century, bog burning culture was a common cultivation system for food production on otherwise non-arable bog peat soils. Burning and preliminary drainage of the peat impacted the soils nutrient supply, bog morphology and soils properties. To gain insights into the long-term effects of bog burning culture on the landscape and soils, a burned and unburned area within a rewetted bog complex were comparatively analysed. It was hypothesised that bog burning had a lasting effect on the soil chemistry, that the trenches created for drainage prior to burning are still detectable in the bog morphology, and that the altered soil chemistry exhibiting enhanced nutrient supply resulted in a change of vegetation patterns. To verify this, the soil chemistry was analysed regarding pH, carbon/nitrogen (C/N) ratio, and contents of plant available phosphate (PO43-) and potassium (K). The morphology was examined by means of aerial imagery and vegetation patterns were assessed in the field. It was shown that while PO43-- contents were similar, pH values and K contents of the burned area were elevated compared with the unburned area. Accordingly, they can be used as an indicator for bog burning culture, even a century after the end of the practice. As expected, C/N ratios were narrowed in the burned area, which however cannot exclusively be attributed to bog burning, since peat mineralisation in the previously drained bog soils caused narrowing C/N ratios as well. The trench structure for drainage was still visible in aerial images and vegetation patterns were similar in the burned and unburned areas. Overall, the aftermath of bog burning was still apparent in morphology and soil chemistry, however the effect was less severe than expected, as vegetation patterns and the overall restoration success were not impacted. This provides a reasonable expectation that bogs are resilient towards bog burning and the latter is no obstacle for successful restoration.

Sources, distribution and decomposition of soil organic matter based on an effective biomarker in the pastoral areas of Zoige Plateau, China

The degradation of organic matter in soils plays an important role in the carbon cycle. Lignin is the main source of soil organics and it can be used to trace the source, distribution and turnover of organic matter. In this study the distribution and degradation of lignin were investigated to identify the source and degradation of soil organic matter during the succession of China's Zoige Plateau. Lignin monomers were determined by gas chromatography-mass spectrometry with alkaline CuO oxidation and the soils' δ13C and δ15N contents were interpreted to explore the turnover rate of lignin and organic matter. The main source of organics was identified as C3 non-woody angiosperm tissues. Lignin in the topsoil (0–30 cm) was derived from litter and roots, and it then migrated vertically to the deep soil (30–80 cm). Correlations of δ13C/δ15N with the soil's elemental composition showed that the organics degraded more quickly in meadow soil than in bog soil. The soil communities in the meadow and bog soils were generally similar, but there were certain differences in the dominant microbial phyla at different depths. The meadow soil's effectiveness as a carbon sink was gradually weakened, while that of the bog soil strengthened with depth. These results provide a scientific basis for accurately assessing the carbon sink capacity of the soils in Zoige Plateau.

Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil.

Studying the minor part of the uncultivated microbial majority ("rare biosphere") is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-3659, Isolated from Commercial Cranberry Bog Soil in Massachusetts, USA.

Pseudomonas sp. strain MWU13-3659 was isolated from cultivated cranberry bog soil in Massachusetts, USA. Its closest known relative is Pseudomonas entomophila (digital DNA-DNA hybridization [d4 formula] value of 57.2% and average nucleotide identity based on BLAST value of 93.90), and its genome contains putative gene clusters for the production of polyketides, siderophores, and cyclic lipopeptides that have insecticidal activity in other proteobacteria.

Draft Genome Sequences of Pseudomonas sp. Strains MWU 12-2029, MWU 12-3088, and MWU 12-3091, Isolated from Wild and Cultivated Massachusetts Cranberry Bogs.

Pseudomonas sp. strains MWU12-2029, MWU12-3088, and MWU12-3091 were isolated from wild and cultivated cranberry bog soils in southeastern Massachusetts. The three isolates are closely related to Pseudomonas kribbensis, a not validly published member of the P. fluorescens group, and contain three putative insecticidal protein genes, including the toxin complex A gene (tcaC).