Conversion from natural wetlands to paddy field alters the composition of soil bacterial communities in Sanjiang Plain, Northeast China

A review of factors affecting the soil microbial community structure in wetlands

Microbial community in wetland soils is crucial for maintaining the stability of the wetland ecosystem. Nevertheless, the soil microbial community is sensitive to the environmental stress in wetlands. This leads to the possibility that the microbial community structure may be influenced by environmental factors. To gain an in-depth understanding in the response of microbial community structure in wetland soils under different environmental factors, this review comprehensively explores the factors of natural conditions (e.g., different types of wetland, soil physical and chemical properties, climate conditions), biological factors (e.g., plants, soil animals), and human activities (e.g., land use, soil pollution, grazing). Those factors can affect microbial community structure and activities in wetland soils through different ways such as (i) affecting the wetland soil environment in which soil microorganisms survived in, (ii) influencing the available nutrients (e.g., carbon, nitrogen) required for microbial activity, and (iii) the direct effects on soil microorganisms (toxicity or promotion of resistant species). This review can provide references for the conservation of microbial diversity in wetland soils, the maintenance of wetland ecosystem balance, and the wetland ecological restoration.

pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China

Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.

Mechanism of downward migration of quinolone antibiotics in antibiotics polluted natural soil replenishment water and its effect on soil microorganisms

Reclaimed water is widely concerned as an effective recharge of groundwater and surface water, but trace organic pollutants produced by traditional wastewater treatment plants (WWTPs) would cause environmental pollution (water and soil) during infiltration. Therefore, the effects of reclaimed water containing ofloxacin (OFL) and ciprofloxacin (CIP) in antibiotics polluted natural soil (APNS) were investigated by simulating soil aquifer treatment systems (SATs). The experiment results showed that OFL and CIP in water were adsorbed and microbially degraded mainly at 30 cm, and the concentration of OFL and CIP in soil increased with depth, which were mainly due to the desorption from APNS. Concurrently, the change in replenishment water concentration also significantly affected OFL and CIP in pore water and soil. Although OFL and CIP inhibited the diversity of soil microbial community, they also promoted the growth of some microorganisms. As the dominant bacteria, Proteobacteria and Acidobacteriota can effectively participate in the degradation of OFL and CIP. The degradation effects of soil microorganisms on OFL and CIP were 45.48% and 42.39%, respectively, indicating that soil microorganisms selectively degraded pollutants. This experiment was carried out on APNS, which provided a reference for future studies on the migration of trace organic pollutants under natural conditions.

Soil physicochemical properties drive the variation in soil microbial communities along a forest successional series in a degraded wetland in northeastern China

The Sanjiang Plain is the biggest freshwater wetland locating in northeastern China. Due to climate change and human activities, that wetland has degraded to a successional gradient from the original flooded wetland to dry shrub vegetation and a forest area with lower ground water level, which may result in changes in soil microbiologic structure and functions. The present study investigated the microbial diversity and community structure in relation to soil properties along that successional gradient. The soil physico-chemical properties changed significantly with degradation stage. The Shannon diversity index of both soil bacteria (5.90-6.42) and fungi (1.7-4.19) varied significantly with successional stage (both p < .05). The community structures of soil bacteria and fungi in the early successional stages (i.e., the wetland) were significantly determined by water content, total nitrogen, and available nitrogen concentrations in soils, while those in the later successional stages (i.e., forests) were significantly structured by soil organic carbon, soil pH, and available phosphorus concentrations. These results suggest that the soil microbial structure is mainly determined by soil properties rather than by plant community such as plant species composition along successional stages.

Trebonia kvetii gen. nov., sp. nov., an acidophilic actinobacterium, and proposal of the new actinobacterial family Treboniaceae fam. nov

A novel actinobacterial strain, designated 15TR583T, was isolated from a waterlogged acidic soil collected near the town of Trebon, Czech Republic, and was subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that the organism forms an individual line of descent related to the orderStreptosporangiales, classActinomycetia. The strain shared highest 16S rRNA gene sequence similarity, yet of only 92.8%, withActinocorallia aureaIFO 14752T. The strain grew in white colonies of aerobic, Gram-stain-positive, unbranching substrate mycelium bearing single spores at hyphae tips. The major fatty acids (>10%) were iso-C16 : 0, C16 : 0, iso-C17 : 1ω9 and 10-methyl-C17 : 0. The fatty acid pattern differed from all patterns currently described for actinobacterial genera. The organism contained as major menaquinones MK9(H6) and MK9(H8), which differentiated it from other actinobacterial families. Polar lipids were composed of six unidentified glycolipids, an unidentified phosphoglycolipid, two unidentified phospholipids and two unidentified aminolipids. Whole-cell sugars contained galactose, xylose and arabinose as major components. The peptidoglycan type was A1γmeso-diaminopimelic acid. The genomic DNA G+C content was 69.7 mol%. The distinct phylogenetic position and unusual combination of chemotaxonomic characteristics justify the proposal ofTreboniagen. nov., with the type speciesTrebonia kvetiisp. nov. (type strain 15TR583T=CCM 8942T=DSM 109105T), withinTreboniaceaefam. nov.

Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China

The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.

Performance and bacterial community structure of a 10-years old constructed mangrove wetland

Constructed mangrove wetland has been used for wastewater treatment but its long-term performance has not been reported. One-year monitoring of a 10-years old horizontal subsurface-flow constructed mangrove wetland consisting of three belts, two with mangrove plants and one without, revealed that the system maintained high and stable removal percentages of organic matter and nutrients, and planted belts performed better than unplanted control. Substrates in belts planted with Aegiceras corniculatum or Kandelia obovata had higher abundance of ammonifiers, nitrifiers and denitrifiers but lower total heterotrophic bacteria than unplanted substrate. Denaturing gradient gel electrophoresis showed that microbial diversity in planted substrate was significantly lower than that in unplanted one. The bacteria in substrates, irrespective to belts, were phylogenetically related to Proteobacteria (most dominant), Acidobacteria, Firmicutes, Nitrospirae, Gemmatimonadetes, Chloroflexi and Cyanobacteria. The steady performance of this 10-year old constructed mangrove wetland was affected by the abundance and diversity of bacterial community in substrate.

Myxobacteria in high moor and fen: An astonishing diversity in a neglected extreme habitat

Increasing antibiotic resistances of numerous pathogens mean that myxobacteria, well known producers of new antibiotics, are becoming more and more interesting. More than 100 secondary metabolites, most of them with bioactivity, were described from the order Myxococcales. Especially new myxobacterial genera and species turned out to be reliable sources for novel antibiotics and can be isolated from uncommon neglected habitats like, for example, acidic soils. Almost nothing is known about the diversity of myxobacteria in moors, except some information from cultivation studies of the 1970s. Therefore, we evaluated the myxobacterial community composition of acidic high moor and fen both with cultivation‐independent 16S rRNA clone bank analysis and with cultivation. Phylogenetic analyses of clone sequences revealed a great potential of undescribed myxobacteria in high moor and fen, whereby all sequences represent unknown taxa and were detected exclusively by cultivation‐independent analyses. However, many clones were assigned to sequences from other cultivation‐independent studies of eubacterial diversity in acidic habitats. Cultivation revealed different strains exclusively from the genus Corallococcus. Our study shows that the neglected habitat moor is a promising source and of high interest with regard to the cultivation of prospective new bioactive secondary metabolite producing myxobacteria.

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

Northern peatlands in general have high methane (CH₄) emissions, but individual peatlands show considerable variation as CH₄ sources. Particularly in nutrient-poor peatlands, CH₄ production can be low and exceeded by carbon dioxide (CO₂) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO₂ to CH₄ produced. After [¹³C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH₄ and CO₂ The oligotrophic fen had lower CH₄ production but produced 3 to 59 times more CO₂ than CH₄ RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH₄ production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO₂ production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH₄ production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO₂ production in peatlands.

IMPORTANCE

Peatlands are major sources of the greenhouse gas methane (CH₄), yet in many peatlands, CO₂ production from unresolved anaerobic processes exceeds CH₄ production. Anaerobic degradation produces the precursors of CH₄ production but also represents competing processes. We show that anaerobic degradation leading to high or low CH₄ production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH₄ production, while novel and unconventional degraders could be identified in a site where CO₂ production greatly exceeds CH₄ production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH₄ production and reveal bacteria potentially producing the excess CO₂ in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH₄ emission from peatlands.

Influence of substrate type on microbial community structure in vertical-flow constructed wetland treating polluted river water

Microorganisms attached on the surfaces of substrate materials in constructed wetland play crucial roles in the removal of organic and inorganic pollutants. However, the impact of substrate material on wetland microbial community structure remains unclear. Moreover, little is known about microbial community in constructed wetland purifying polluted surface water. In this study, Illumina high-throughput sequencing was applied to profile the spatial variation of microbial communities in three pilot-scale surface water constructed wetlands with different substrate materials (sand, zeolite, and gravel). Bacterial community diversity and structure showed remarkable spatial variation in both sand and zeolite wetland systems, but changed slightly in gravel wetland system. Bacterial community was found to be significantly influenced by wetland substrate type. A number of bacterial groups were detected in wetland systems, including Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Cyanobacteria, Nitrospirae, Planctomycetes, Actinobacteria, Firmicutes, Chlorobi, Spirochaetae, Gemmatimonadetes, Deferribacteres, OP8, WS3, TA06, and OP3, while Proteobacteria (accounting for 29.1-62.3 %), mainly composed of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, showed the dominance and might contribute to the effective reduction of organic pollutants. In addition, Nitrospira-like microorganisms were abundant in surface water constructed wetlands.