Resilience of methane cycle and microbial functional genes to drought and flood in an alkaline wetland: A metagenomic analysis

Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis

Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession.

IMPORTANCE

Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.

Metagenomic insights into carbon and nitrogen cycling in the water-land transition zone of inland alkaline wetlands

Inland alkaline wetlands play a crucial role in maintaining ecological functions. However, these wetlands are becoming more vulnerable to the effects of water level fluctuations caused by global climate change, especially concerning carbon (C) and nitrogen (N) cycling. Here, metagenomics sequencing was used to investigate microorganism diversity, C and N cycling gene abundance at three water level types (D (dry), MF (middle flooded), HF (high flooded)) along an inland alkaline wetland. Our findings reveal that water level was the most important factor in regulating the microbial communities. Distinct shifts in community composition were found along the water level increases, without fundamentally altering their composition. With the increase of water level, the relative abundance of pmoA decreased from 2.5 × 10-5 to 5.1 × 10-6. The C cycling processes shift from predominantly CO2-generated processes under low water levels to CO2 and CH4 co-generated processes under high water levels. The relative abundance of nosZ reached 4.9 × 10-5 in HF, while in D and MF, it is recorded at 4.5 × 10-5 and 3.4 × 10-5, respectively. Water levels accelerate N cycling and generating N2O intermediates. Furthermore, our study highlights the dynamic competition and cooperation between C and N cycling processes. This research provides a comprehensive biological understanding of the influence of varying water levels on soil C and N cycling processes in wetland.

Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

Effects of periodic drying-wetting on microbial dynamics and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in intertidal wetland sediments

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH₄) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH₄, which may help accurately project CH₄ emission from intertidal wetlands under different tidal scenarios.

Response of vegetation dynamic change to multi-scale drought stress in the high-latitude Nenjiang River basin in China

Vegetation is an integral part of terrestrial ecosystem and plays an important role in responding to climate change, with its dynamic characteristics reflecting the ecological environmental quality. Recently, the continually increasing frequency and intensity of droughts has greatly changed how vegetation growth and development respond to drought. In this study, using normalized difference vegetation index and standardized precipitation evapotranspiration index (SPEI), we studied the response characteristics of vegetation dynamics to multi-scale drought stress (SPEI-1, SPEI-3, and SPEI-12) in the Nenjiang River basin (NRB) via Pearson correlation analysis, along with further exploration of the vegetation stability under drought. The results showed that the same period effect of drought on vegetation growth in NRB mainly occurs during the early and middle stages of vegetation growth. Furthermore, the proportion of significant positive correlation between them is 15.3%–43.3%, mainly in the central and southern parts of the basin. The lagged period effect of drought on vegetation growth mainly occurred during autumn in the southeast and middle of the basin, with a significant positive correlation of 20.8%. Under drought stress, the forest vegetation stability in NRB was the highest, with the resilience of wetland and grassland vegetation being the best and worst, respectively. Our study results will not only deepen our understanding of the dynamic vegetation changes in the high-latitude semi-arid basin under global climate change, but also provide a scientific basis for the management and water resources allocation of “agriculture-wetland-forest” complex ecosystem in the future.

Effects of water regimes on soil N2O, CH4 and CO2 emissions following addition of dicyandiamide and N fertilizer

Water regimes strongly impact soil C and N cycling and the associated greenhouse gases (GHGs, i.e., CO₂, CH₄ and N₂O). Therefore, a study was conducted to examine the impacts of flooding-drying of soil along with application of nitrogen (N) fertilizer and nitrification inhibitor dicyandiamide (DCD) on GHGs emissions. This study comprised four experimental treatments, including (i) control (CK), (ii) dicyandiamide, 20 mg kg^-1 (DCD), (iii) nitrogen fertilizer, 300 mg kg^-1 (N) and (iv) DCD + N. All experimental treatments were kept under flooded condition at the onset of the experiment, and then converted to 60% water filled pore space (WFPS). At flooding stage, N₂O emissions were lower as compared to 60% WFPS. The highest cumulative N₂O emission was 0.98 mg N₂O-N kg^-1 in N treated soil due to high substrates of mineral N contents, but lowest (0.009 mg N₂O-N kg^-1) in the DCD treatment. The highest cumulative CH₄ emissions (80.54 mg CH₄-C kg^-1) were observed in the N treatment, while uptake of CH₄ was observed in the DCD treatment. As flooded condition converted to 60% WFPS, CO₂ emissions gradually increased in all experimental treatments, but the maximum cumulative CO₂ emission was 477.44 mg kg^-1 in the DCD + N treatment. The maximum dissolved organic carbon (DOC) contents were observed in N and DCD + N treatments with the values of 57.12 and 58.92 mg kg^-1, respectively. Microbial biomass carbon (MBC) contents were higher at flooding while lower at transition phase, and increased at the initiation of 60% WFPS stage. However, MBC contents declined at the later stage of 60% WFPS. The maximum MBC contents were 202.12 and 192.41 mg kg^-1 in N and DCD + N treatments, respectively. Results demonstrated that water regimes exerted a dramatic impact on C and N dynamics, subsequently GHGs, which were highly controlled by DCD at both flooding and 60% WFPS conditions.

Removal of organochlorine pesticides and metagenomic analysis by multi-stage constructed wetland treating landfill leachate

Constructed wetlands (CWs) can effectively treat landfill leachate (LL). However, there is limited research on the removal of organochlorine pesticides (OCPs) refractory organics during LL treatment in CWs. In this study, multi-stage subsurface flow CWs was used to treat LL, and the removal fate of hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) in CWs was investigated. The structural differences between plant roots and substrate microbial communities were compared and the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway of organic matter was analyzed based on metagenomic analysis. The results showed that substrate adsorption (50.55%-72.74%) and microbial degradation (20.38%-27.89%) were the main ways to remove OCPs. The Proteobacteria occupied a dominant position in the CWs system, among which Betaproteobacteria (34.37%-35.90%) were contained in the substrate, and Alphaproteobacteria (21.19%-23.84%) was a more dominant microorganism in plant roots. Formaldehyde assimilation and serine pathway were the main pathways of methane metabolism. This study provides a reference for the removal mechanism of OCPs to promote the application of CWs technology in LL treatment.

Exogenous N-hexanoyl-L-homoserine lactone assists in upflow anaerobic sludge blanket recovery from acetate accumulation via aceticlastic methanogens enrichment

Volatile fatty acids (VFAs) accumulation caused by shock loading severely hampers the performance and stability of anaerobic digestion. An upflow anaerobic sludge blanket (UASB) was operated to examine its performance, sludge properties, and microbial community behavior during shock loading and recovery with exogenous N-hexanoyl-L-homoserine lactone (C₆-HSL). After shock loading, chemical oxygen demand (COD) removal was significantly reduced from 79.09% to 65.63%. The abundance of Methanosarcinales also significantly decreased, which resulted in acetate accumulation (1,163.55 mg/L). Sludge granules disintegrated along with the decrease in extracellular polymeric substances (EPS). After supplying 1 μg/L C₆-HSL, COD removal resumed to 75.10%. Furthermore, C₆-HSL enhanced the abundance and metabolic activity of aceticlastic methanogens, decreased acetate concentration to 146.87 mg/L, improved EPS secretion, and caused the re-assembly of disintegrated sludges to form large granules. These results advanced our understanding of microbial community behavior and provided an attractive strategy for restoration of UASB recovered from shock loading.