Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments

Spartina alterniflora invasion reduces soil microbial diversity and weakens soil microbial inter-species relationships in coastal wetlands

Soil microorganisms play a crucial role in the plant invasion process, acting as both drivers of and responders to plant invasion. However, the effects of plant invasion on the complexity and stability of co-occurrence networks of soil microbial communities remain unclear. Here, we investigated how the invasion of Spartina alterniflora affected the diversity, composition, and co-occurrence networks of soil bacterial and fungal communities in the Yellow River Delta, China. Compared to the native plant (Suaeda salsa), S. alterniflora invasion decreased the α-diversity of soil bacterial communities but did not affect that of fungal communities. The β-diversity of soil bacterial and fungal communities under S. salsa and S. alterniflora habitats also differed dramatically. S. alterniflora invasion increased the relative abundance of the copiotrophic phylum Bacteroidota, whereas decreased the relative abundances of the oligotrophic phyla Acidobacteriota and Gemmatimonadota. Additionally, the relative abundance of Chytridiomycota, known for its role in degrading recalcitrant organic matter, increased substantially within the soil fungal community. Functional predictions revealed that S. alterniflora invasion increased the relative abundance of certain soil bacteria involved in carbon and nitrogen cycling, including aerobic chemoheterotrophy, nitrate reduction, and nitrate respiration. More importantly, S. alterniflora invasion reduced the complexity and stability of both soil bacterial and fungal community networks. The shifts in soil microbial community structure and diversity were mainly induced by soil available nutrients and soil salinity. Overall, our study highlights the profound impacts of S. alterniflora invasion on soil microbial communities, which could further indicate the modification of ecosystem functioning by invasive species.

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

Invasion mechanism of Spartina alterniflora by regulating soil sulfur and iron cycling and microbial composition in the Jiuduansha Wetland

Spartina alterniflora, an invasive plant widely distributed in China's coastal regions, has had a significant impact on the stability of wetland ecosystems and elemental biogeochemical cycles. The invasion of S. alterniflora has been found to lead to the accumulation of sulfides in the soil. The cycling of sulfur and iron in the soil is closely interconnected. Coastal estuarine wetlands are influenced by both freshwater in rivers and seawater tides, as well as the frequent variations in redox conditions caused by tidal fluctuations, which makes the cycling of sulfur and iron in the soil invaded by S. alterniflora more intricate. In this study, field surveys and laboratory experiments were conducted to explore the effects of S. alterniflora invasion and hydrological changes on the cycling of sulfur and iron as well as related functional microorganisms in the soil. The invasion of S. alterniflora showed an increase in soil reduced inorganic sulfur (RIS) components in both high and low marshes of Jiuduansha wetland, with higher content observed in summer and autumn. The tidal simulation experiments revealed abundant sulfate in seawater tidal conditions could promote the formation of acid volatile sulfides (AVS) in the soil of low marshes invaded by S. alterniflora and ensuring the continuous increase in AVS content. Diffusive gradients in-thin-films (DGT) technology indicated the existence of high-concentration soluble S2- enrichment zones in the soil of low marshes invaded by S. alterniflora, which may be related to S. alterniflora root exudates. Tidal action increased the relative abundance of sulfur-reducing bacteria (SRB) in the soil of low marshes, and under the influence of seawater tidal action, SRB exhibited higher relative abundance. However, S. alterniflora might inhibit the activity of iron-reducing bacteria (FeRB) in the soil of low marshes. In conclusion, S. alterniflora may enhance the sulfate reduction rate and promote the formation of free sulfides in tidal salt marsh ecosystems by releasing root exudates that stimulate the activity of SRB, while concurrently inhibiting the activity of FeRB and reducing their competition with SRB. This effect is particularly pronounced in low marshes under seawater tidal conditions. Thus, S. alterniflora is capable of rapidly invading tidal salt marshes by utilizing sulfides effectively.

High methane concentrations in tidal salt marsh soils: Where does the methane go?

Tidal salt marshes produce and emit CH4 . Therefore, it is critical to understand the biogeochemical controls that regulate CH4 spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH4 production, and higher salinity concentrations inhibit CH4 production in salt marshes. Recent evidence shows that CH4 is produced within salt marshes via methylotrophic methanogenesis, a process not inhibited by sulfate reduction. To further explore this conundrum, we performed measurements of soil-atmosphere CH4 and CO2 fluxes coupled with depth profiles of soil CH4 and CO2 pore water gas concentrations, stable and radioisotopes, pore water chemistry, and microbial community composition to assess CH4 production and fate within a temperate tidal salt marsh. We found unexpectedly high CH4 concentrations up to 145,000 μmol mol-1 positively correlated with S2- (salinity range: 6.6-14.5 ppt). Despite large CH4 production within the soil, soil-atmosphere CH4 fluxes were low but with higher emissions and extreme variability during plant senescence (84.3 ± 684.4 nmol m-2  s-1 ). CH4 and CO2 within the soil pore water were produced from young carbon, with most Δ14 C-CH4 and Δ14 C-CO2 values at or above modern. We found evidence that CH4 within soils was produced by methylotrophic and hydrogenotrophic methanogenesis. Several pathways exist after CH4 is produced, including diffusion into the atmosphere, CH4 oxidation, and lateral export to adjacent tidal creeks; the latter being the most likely dominant flux. Our findings demonstrate that CH4 production and fluxes are biogeochemically heterogeneous, with multiple processes and pathways that can co-occur and vary in importance over the year. This study highlights the potential for high CH4 production, the need to understand the underlying biogeochemical controls, and the challenges of evaluating CH4 budgets and blue carbon in salt marshes.

Impact of Spartina alterniflora Invasion in Coastal Wetlands of China: Boon or Bane?

Invasive plants, like Spartina alterniflora (SA), have a competitive advantage over native flora due to their rapid utilization of vital soil nutrients. This results in the depletion of resources for native plant species, significantly impacting ecosystem diversity and stability. This comprehensive review addresses several key aspects related to SA's spread and spatial distribution in China's wetlands. The rapid expansion of Spartina alterniflora is attributed to its high reproductive ability, adaptability to environmental factors like elevated salinity, and ability to disperse its seeds via tides. Spartina alterniflora mainly were found in Zhejiang, Jiangsu, Fujian, and Shanghai provinces, accounting for more than 90% of China's total Spartina alterniflora area. Spartina alterniflora rapid growth results in displacement of native species and loss of vital microbial, plant, and animal diversity. Some studies reported that Spartina alterniflora increases carbon storage, while others argue that it weakens this function. The impact of Spartina alterniflora on organic and inorganic carbon requires further research for better understanding dynamics of carbon in coastal wetlands. The controlled growth of Spartina alterniflora can be beneficial in many aspects of the coastal wetlands' ecosystem. In China, various methods have been employed to control the invasion of SA. Physical control, such as removing the plants and converting them into fertilizer or bioenergy, has been commonly used but has limitations like air pollution and the potential for re-invasion. Chemical herbicides like Imazapyr and Haloxyfop-R-methyl have effectively controlled and prevented re-invasion in specific areas, but their potential adverse impacts are still uncertain. Wetland Park construction, aquaculture development, and substituting native or exotic species with mangroves or reed communities have also been successful. It becomes evident that a long-standing and Contextual approach is necessary to effectively manage the advantages and curtail the drawbacks associated with S. alterniflora across China.

Sulfate reduction behavior in pressure-bearing leachate saturated zone

Attention should be paid to the sulfate reduction behavior in a pressure-bearing leachate saturated zone. In this study, within the relative pressure range of 0-0.6 MPa, the ambient temperature with the highest sulfate reduction rate of 50°C was selected to explore the difference in sulfate reduction behavior in a pressure-bearing leachate saturated zone. The results showed that the sulfate reduction rate might further increase with an increase in pressure; however, owing to the effect of pressure increase, the generated hydrogen sulfide (H₂S) could not be released on time, thereby decreasing its highest concentration by approximately 85%, and the duration extended to about two times that of the atmospheric pressure. Microbial community structure and functional gene abundance analyses showed that the community distribution of sulfate-reducing bacteria was significantly affected by pressure conditions, and there was a negative correlation between disulfide reductase B (dsrB) gene abundance and H₂S release rate. Other sulfate reduction processes that do not require disulfide reductase A (dsrA) and dsrB genes may be the key pathways affecting the sulfate reduction rate in the pressure-bearing leachate saturated zone. This study improves the understanding of sulfate reduction in landfills as well as provides a theoretical basis for the operation and management of landfills.

Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion

Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.

Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea

Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO₃ ^-), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.

Microbial respiratory thermal adaptation is regulated by r-/K-strategy dominance

Microbial thermal adaptation is considered to be one of the core mechanisms affecting soil carbon cycling. However, the role of microbial community composition in controlling thermal adaptation is poorly understood. Using microbial communities from the rhizosphere and bulk soils in an 8-year warming experiment as a model, we experimentally demonstrate that respiratory thermal adaptation was much stronger in microbial K-strategist-dominated bulk soils than in microbial r-strategist-dominated rhizosphere soils. Soil carbon availability exerted strong selection on the dominant ecological strategy of the microbial community, indirectly influencing respiratory thermal adaptation. Our findings shed light on the linchpin of the dominant ecological strategy exhibited by the microbial community in determining its respiratory thermal adaptation, with implications for understanding soil carbon losses under warming.

Exogenous nitrogen from riverine exports promotes soil methane production in saltmarshes in China

Methane emissions from saltmarshes can potentially promote climate warming. Soil methane production is positively correlated with methane emissions from saltmarshes. Understanding the factors influencing soil methane production will improve the prediction of methane emissions, but an investigation of these factors has not been conducted in saltmarshes in China. We collected soils from native Phragmites australis and invasive Spartina alterniflora saltmarshes along the coast of China; the soil potential methane production (PMP) was determined by incubation experiments. The large-scale investigation results showed that the ratios of methanogens relative to sulfate-reducing bacteria (RMRS) and total organic carbon (TOC) were positively correlated with soil PMP for both species. Dissolved inorganic nitrogen (DIN) was positively correlated with the soil PMP of P. australis saltmarshes, and plant biomass was positively correlated with the soil PMP of S. alterniflora saltmarshes. Our results showed that exogenous nitrogen from riverine exports was positively correlated with DIN and plant biomass in both P. australis and S. alterniflora saltmarshes. In addition, exogenous nitrogen was also positively correlated with TOC in S. alterniflora saltmarshes. Consequently, exogenous nitrogen indirectly promoted soil methane production in P. australis saltmarshes by increasing the DIN and promoted soil methane production in S. alterniflora saltmarshes by enhancing the TOC and plant biomass. Moreover, we found that the promoting effect of DIN on the soil PMP of P. australis saltmarshes increased when the incubation temperature increased from 15 °C to 25 °C. Thus, the promoting effect of exogenous nitrogen on the soil methane production in P. australis saltmarshes might be strengthened in the peak of growing season. Our findings are the first to confirm that exogenous nitrogen inputs from rivers indirectly promote soil methane production in P. australis and S. alterniflora saltmarshes and provide new insights into the factors responsible for soil methane production in saltmarshes.

Soil Bacterial Community Structure in Different Micro-Habitats on the Tidal Creek Section in the Yellow River Estuary

Tidal creeks have attracted considerable attention in estuary wetland conservation and restoration with diverse micro-habitats and high hydrological connectivity. Bacterial communities act effectively as invisible engines to regulate nutrient element biogeochemical processes. However, few studies have unveiled the bacterial community structures and diversities of micro-habitats soils on the tidal creek section. Our study selected three sections cross a tidal creek with obviously belt-like habitats “pluff mudflat – bare mudflat – Tamarix chinensis community – T. chinensis-Suaeda salsa community– S. salsa community” in the Yellow River estuarine wetland. Based on soil samples, we dissected and untangled the bacterial community structures and special bacterial taxa of different habitats on the tidal creek section. The results showed that bacterial community structures and dominant bacterial taxa were significantly different in the five habitats. The bacterial community diversities significantly decreased with distance away from tidal creeks, as well as the dominant bacteria Flavobacteriia and δ-Proteobacteria, but in reverse to Bacteroidetes and Gemmatimonadetes. Moreover, the important biomarkers sulfate-reducing bacteria and photosynthetic bacteria were different distributions within the five habitats, which were closely associated with the sulfur and carbon cycles. We found that the bacterial communities were heterogeneous in different micro-habitats on the tidal creek section, which was related to soil salinity, moisture, and nutrients as well as tidal action. The study would provide fundamental insights into understanding the ecological functions of bacterial diversities and biogeochemical processes influenced by tidal creeks.

Spartina alterniflora invasion has a greater impact than non-native species, Phragmites australis and Kandelia obovata, on the bacterial community assemblages in an estuarine wetland

The invasion of Spartina alterniflora poses a serious threat to the sustainability of native ecosystems worldwide. However, compared with other non-native plants (e.g., Phragmites australis and Kandelia obovata), how Spartina alterniflora invasion influences the community structure of bacteria and their assembly processes and functionality remains elusive. Here, we characterized the diversity, community structure, assembly processes and functional guilds of bacteria underneath five plant species and a bare tidal flat at three soil depths in an estuarine wetland. We found that plant species played a more important role than soil depth in mediating the bacterial community structure. Compared with bare tidal flats, the native species Cyperus malaccensis, rather than Scirpus triqueter, significantly changed the bacterial community structure. However, S. alterniflora invasion increased bacterial alpha diversity and significantly altered the bacterial community structure by enriching Chloroflexi, Bacteroidetes and Firmicutes while reducing Acidobacteria, Nitrospirae and Gemmatimonadetes. The invasion of P. australis and translocation of K. obovata had less pronounced effects on the bacterial community structure. Total carbon, total nitrogen and salinity were the key environmental factors mediating the bacterial community structure. Overall of all the non-native plant species, the invasion of S. alterniflora increased the relative importance of stochastic processes in the assembly of bacterial communities, and shifted the bacterial functional profiles by stimulating sulfur cycling groups and suppressing nitrogen cycling groups. Altogether, our results suggest that S. alterniflora invasion has a greater effect than P. australis invasion or K. obovata translocation on the profiles and assembly processes of the bacterial communities, with important implications for soil biogeochemical processes in coastal wetlands.

Spartina alterniflora Invaded Coastal Wetlands by Raising Soil Sulfur Contents: A Meta-Analysis

Nowadays, plant invasion has become a global ecological threat to local biodiversity and ecosystem stability. Spartina alterniflora encroaches on the ecological niches of local species and changes the soil’s nutrient cycle. However, few comprehensive assessments focus on the effects of S. alterniflora invasion. Here, we investigated how soil sulfur changed with spatiotemporal variation and life forms of native species after S. alterniflora invasion and speculated the possible mechanism of the sulfur increase based on the references. The invasion of S. alterniflora increased soil total sulfur by 57.29% and phytotoxic sulfide by 193.29%. In general, the invasion of S. alterniflora enhanced the total plant biomass and soil nutrients, e.g., soil organic carbon, total nitrogen, and soil microbial biomass carbon, further increasing soil sulfur content. The sulfur accumulation caused by S. alterniflora might result in the poisoning of native species. Thus, we hypothesized that the success of S. alterniflora invasion was closely connected with soil sulfur, especially toxic sulfide. Our study suggests that researchers should give more attention to the correlation between S. alterniflora invasion and the soil sulfur increase. More research is needed to investigate the mechanisms of the successful invasion by accumulating phytotoxic sulfide.

Role of sulfur biogeochemical cycle in mercury methylation in estuarine sediments: A review

Estuaries are sinks for mercury, in which the most toxic mercury form, neurotoxic methylmercury (MeHg), is produced by mercury methylators and accumulates in estuarine sediments. In the same area, the microbial sulfur cycle is triggered by sulfate-reducing bacteria (SRB), which is considered as the main mercury methylator. In this review, we analyzed the sulfur and mercury speciation in sediments from 70 estuaries globally. Abundant mercury and sulfur species were found in the global estuarine sediments. Up to 727 μg THg/g dw and 880 ng MeHg/g dw were found in estuarine sediments, showing the serious risk of mercury to aquatic ecological systems. Significant correlations between sulfur and MeHg concentrations were discovered. Especially, the porewater sulfate concentration positively correlated to MeHg production. The sulfur cycle affects MeHg formation via activating mercury methylator activities and limiting mercury bioavailability, leading to promote or inhibit MeHg formation at different sulfur speciation concentrations. These results suggest that sulfur biogeochemical cycle plays an important role in mercury methylation in estuarine sediments, and the effect of the sulfur cycle on mercury methylation deserves to be further explored in future research.

Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland

Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.

Influence of inoculum selection on the utilisation of volatile fatty acid and glucose in sulfate reducing reactors

The capacity of three inocula (sewer biofilm, mangrove and estuary sediment) to utilise typical fermentation products of municipal solid waste for biological sulfate reduction was investigated. Each inoculum was used in two reactors, one fed a mixture of volatile fatty acids and another fed glucose to provide a suite of fermentation products via naturally occurring fermentation. Following 228 days of reactor operation, reactors inoculated with mangrove and estuary sediments exhibited higher sulfate reducing efficiencies (80-88%) compared to the biofilm-inoculated reactors (32-49%). Minimal use of acetate and its accumulation in the biofilm-inoculated reactors pointed to the high abundance of incomplete-oxidising sulfate reducing bacteria (SRB), Desulfovibrio and Desulfobulbus (90-96% of the sulfate reducing population). Although Desulfovibrio was also prominent in reactors inoculated with mangrove and estuary sediments, Desulfobacter, a known acetoclastic sulfate reducer, emerged from trace levels in these sediment (0.01% abundance in the estuary sediments and below detection in the mangrove sediments) to comprise 14%-70% of the sulfate reducing population at the end of reactor operation.

Seasonal variations in soil physicochemical properties and microbial community structure influenced by Spartina alterniflora invasion and Kandelia obovata restoration

Spartina alterniflora invasion has initiated one of the greatest changes to occur in coastal wetlands in China, and ecological replacement using mangrove species such as Kandelia obovata is an effective method for controlling these invasions. The effects of S. alterniflora invasions and subsequent K. obovata restorations on soil microbial community structures in different seasons are still not fully understood. In this study, soil samples were collected from six vegetation types (unvegetated mudflat, invasive S. alterniflora stands, one-/eight-/ten-year K. obovata restoration areas, and native mature K. obovata forests) in summer and winter. The variations in the soil microbial community structure between the vegetation types across two seasons were then characterized based on 16S rRNA gene sequencing, and the physicochemical properties that shaped the microbial communities were also determined. The invasion and restoration processes significantly influenced microbial community diversity, composition, and putative functions in different seasonal patterns. Microbial communities from a ten-year restoration area and a native mature K. obovata area shared more similarities than other areas. In both seasons, the key environmental factors driving microbial community included total carbon and nitrogen content, the ratio of carbon to nitrogen, and the soil pH. In addition, total sulfur and total phosphorus contents significantly contributed to structuring microbial communities in summer and winter, respectively. This study provides insights into microbial diversity, composition, and functional profiles in association with physicochemical impacts, with the aim of understanding microbial ecological functions during the invasion and restoration processes in wetland ecosystems.

Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary

Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH₄⁺ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.

New Arsenite Oxidase Gene (aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing

Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5'-ATC TGG GGB AAY RAC AAY TA-3') and 1548R (5'-TTC ATB GAS GTS AGR TTC AT-3'), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.

Advantageous microbial community development and improved performance of pilot-scale field systems treating high-risk acid mine drainage with crab shell

Microbial communities are crucial to the effectiveness and stability of bioremediation systems treating acid mine drainage (AMD); however, little research has addressed how they correlate to system performance under changing environmental conditions. In this study, 16S rRNA gene sequencing and quantitative PCR (qPCR) were used to characterize microbial communities within different substrate combinations of crab shell (CS) and spent mushroom compost (SMC) and their association with chemical performance in pilot-scale vertical flow ponds (VFPs) treating high risk AMD in central Pennsylvania over 643 days of operation. As compared to a control containing SMC, VFPs containing CS sustained higher alkalinity, higher sulfate-reducing rates, and more thorough metals removal (>90% for Fe and Al, >50% for Mn and Zn). Correspondingly, CS VFPs supported the growth of microorganisms in key functional groups at increasing abundance and diversity over time, especially more diverse sulfate-reducing bacteria. Through changing seasonal and operational conditions over almost two years, the relative abundance of the core phyla shifted in all reactors, but the smallest changes in functional gene copies were observed in VFPs containing CS. These results suggest that the high diversity and stability of microbial communities associated with CS are consistent with effective AMD treatment.

Dramatic change of bacterial assembly process and co-occurrence pattern in Spartina alterniflora salt marsh along an inundation frequency gradient

Exotic Spartina alterniflora has become widely distributed along most of the coastlines in China in a wide range of inundation frequencies. However, the assembly processes and co-occurrence patterns of the bacterial community in S. alterniflora wetlands under different inundation frequencies remain elusive. In this study, an in-situ mesocosm was established to investigate the changes in soil bacterial community. We found that soil water content was the most decisive factor in influencing the bacterial community. Balanced variation, rather than abundance gradients, accounted for the major shifts in bacterial communities and was significantly and positively correlated with the changes in water content, suggesting that species substitution was facilitated by the increased water content. Deterministic processes were dominant in community assembly, and a large degree of change in water content increased variable selection. Co-occurrence network revealed that increasing water content significantly decreased the average degree and the relative abundance of keystone species, resulting in a network with less complexity. Structural equation modelling suggests that increasing inundation frequency has strong impacts on bacterial community, primarily by altering water content, network degree, and the relative abundance of keystone species. Overall, our results illustrate that increasing inundation frequency significantly influences the bacterial community assembly processes and co-occurrence patterns.

Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA

Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.

Characterization of bacterial communities associated with the exotic and heavy metal tolerant wetland plant Spartina alterniflora

Heavy metal pollution has seriously disrupted eco-balance and transformed estuaries into sewage depots. Quanzhou bay is a typical heavy metal-contaminated estuary, in which Spartina alterniflora has widely invaded. Plant-associated microbial communities are crucial for biogeochemical cycles, studies of which would be helpful to demonstrate the invasion mechanisms of plants. Meanwhile, they are indispensable to phytoremediation by enhancing the heavy metal tolerance of plants, facilitating heavy metal absorption rate and promoting growth of plants. In the present study, S. alterniflora-associated rhizo- and endobacterial communities from 3 experimental sites were investigated by 454-pyrosequencing. Heavy metal screening generated 16 culturable isolates, further biochemical assays suggested these clones possess various abilities such as phosphate solubilization, indole-3-acetic acid (IAA) production and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production to accelerate heavy metal uptake and growth of the host. This study revealed the bacterial community structures and characterized the predominant resident bacterial strains of S. alterniflora-associated rhizo- and endobacteria under heavy metal stress, and isolated several bacterial species with potential ecological function.

Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh

Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.

Bacterial Succession in Salt Marsh Soils Along a Short-term Invasion Chronosequence of Spartina alterniflora in the Yellow River Estuary, China

As an exotic plant species, Spartina alterniflora seriously threatens native ecosystem function in Chinese coastal regions. Unveiling the dynamics of soil bacteria community during its invasion is essential for a better understanding of related biogeochemical processes, while the shift in soil bacterial community over invasive time remains unclear. A short-term chronosequence was identified to assess the impacts of Spartina alterniflora invasion on soil nutrients and bacterial community composition and structure (using 16S rRNA gene high-throughput sequencing) over the time of invasion (i.e., (1) at least 10 years, (2) nearly 5 years, (3) less than 2 years, and (4) in native salt marshes or 0 years) in the Yellow River Estuary. The results exhibited an orderly change in the soil physicochemical properties and bacterial community composition over the invasion time. Soil pH showed a significant decrease with the accumulation of soil organic matter (SOM), whereas soil nutrients such as soil dissolved organic carbon (DOC), total nitrogen (TN), nitrate (NO₃^-), ammonium (NH₄⁺), K⁺, and Mg²⁺ were generally increased with the age of the invasion. The number of operational taxonomic units (OTUs, 97% similarity level) exhibited a decreasing trend, which suggested a decline in bacterial diversity with the invasion age. The dominant groups at the phylum level were Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes (the sum of relative abundance was > 70% across all samples). The relative abundances of Chloroflexi and Gemmatimonadetes steadily decreased, while the abundance of Bacteroidetes significantly increased with the plant invasion. The distribution pattern of the soil bacteria was clearly separated according to the principal coordinate analysis (PCoA) and canonical correspondence analysis (CCA) in native and invaded salt marshes. The variation in the soil bacterial community was tightly associated with the soil physicochemical properties (Mantel test, P < 0.05). Variance partitioning analysis (VPA) showed that plant traits explained 4.95% of the bacterial community variation, and soil variables explained approximately 26.96% of the variation. Network analysis also revealed that plant invasion strengthens the interaction among soil bacterial communities. Overall, our findings highlight the bacterial community succession during the Spartina alterniflora invasion in coastal salt marsh soils, which can provide insight regarding the association between soil development and invasive plant.

Microbial mechanism for enhanced methane emission in deep soil layer of Phragmites-introduced tidal marsh

The introduction of Phragmites australis is known to substantially increase methane emission in the tidal salt marsh. Previous studies suggested that enhanced carbon input by the introduction may stimulate methanogenic activity. However, the exact mechanisms and the effects of the introduction of P. australis to methane dynamics in the deep soil layer are still unclear. In this study we collected 1 m deep intact soil cores and gas samples at native Suaeda japonica- and P. australis-vegetated temperate tidal salt marshes in Suncheon Bay, Republic of Korea. Rates of methane emission and vertical distribution of soil biogeochemistry and microbial communities were analyzed to understand the relationship among chemical and microbiological properties. The introduction of P. australis significantly enhanced methane emission in sites, which was caused by increased DOC and reduced competitive inhibition between sulfate reducer and methanogens. In particular, reduced competitive inhibition between sulfate reducers and methanogens in deep soil layer may play a substantial role in the enhanced methane emission by the introduction of P. australis. Potential methane production was also significantly higher in deeper soil layers than the surface soil layer. We suggest that deep soil layer plays a critical role in the methane dynamics of tidal salt marsh which is introduced by deep root plants, such as P. australis.

A Bioinformatics Guide to Plant Microbiome Analysis

Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China

In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.

Sulphate-reducing bacteria (SRB) in the Yangtze Estuary sediments: Abundance, distribution and implications for the bioavailibility of metals

Ubiquitous in the aquatic environment, sulphate-reducing bacteria (SRB) are considered one of the dominant microorganisms involved in the degradation of sulphate. This study focused on the spatial and temporal distributions of SRB in the Scirpus triquter rhizosphere sediments with a comparison to non-rhizosphere sediments and evaluated the implication of SRB to the bioavailability of metals in the Yangtze Estuary. The results showed that taking dsrB as the target gene, SRB abundances in rhizosphere sediments were significantly higher than those in non-rhizosphere sediments (P<0.01). SRB abundances were relatively higher in April and January than other seasons. Moreover, redundancy discriminate analysis (RDA) results indicated that sulphate, pH and TOC were the major environmental factors affecting the SRB abundance in rhizosphere sediments. The concentrations of most metals were significantly related to SRB abundance, and sulphide concentrations showed a significantly positive correlation to metal concentrations, indicating metal sulphide/metal associated sulphide could be regulated by SRB. Furthermore, electron microscope analysis found that nano-sized metal sulphide particles were ubiquitous in rhizosphere sediments and could be further taken up by plants. This study provides new insights into the immobilization and removal of heavy metals and the ecological value of the sulphate-reducing bacteria in the Yangtze Estuary.

Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China's wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

Exotic Spartina alterniflora invasion increases CH4 while reduces CO2 emissions from mangrove wetland soils in southeastern China

Mangroves are critical in global carbon budget while vulnerable to exotic plant invasion. Spartina alterniflora, one of typical salt marsh plant grows forcefully along the coast of China, has invaded the native mangrove habitats in Zhangjiang Estuary. However, the effects of S. alterniflora invasion on soil carbon gases (CH₄ and CO₂) emission from mangroves are not fully understood. Accordingly, we conducted a field experiment to investigate the soil CH₄ and CO₂ emission during growing seasons in 2016 and 2017 at four adjacent wetlands, namely bare mudflat (Mud), Kandelia obovata (KO), Avicennia marina (AM) and S. alterniflora (SA). Potential methane production (PMP), potential methane oxidation (PMO), functional microbial abundance and soil biogeochemical properties were measured simultaneously. Our results indicate that S. alterniflora invasion could dramatically increase soil CH₄ emissions mainly due to the enhancement in PMP which facilitated by soil EC, MBC, TOC and mcrA gene abundance. Additionally, S. alterniflora invasion decreases soil CO₂ emission. Both heterotrophic microbial respiration (16S rRNA) and methane oxidation (pmoA and ANME-pmoA) are responsible for CO₂ emission reduction. Furthermore, S. alterniflora invasion greatly increases GWP by stimulating CH₄ emissions. Thus, comparing with mangroves, invasive S. alterniflora significantly (p < 0.001) increases CH₄ emission while reduces CO₂ emission.

Dry-wet cycles of kettle hole sediments leave a microbial and biogeochemical legacy

Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO₂-outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

A new method for the simultaneous enhancement of methane yield and reduction of hydrogen sulfide production in the anaerobic digestion of waste activated sludge

The biogas generated from anaerobic digestion (AD) also includes undesirable by-product such as hydrogen sulfide (H₂S), which must be removed before the biogas can be used as a clean energy source. Therefore, it is necessary to find an appropriate strategy to simultaneously enhance the methane yield and reduce H₂S production. An efficient strategy-pretreating sludge at pH 10 for 8d and adjusting the system at neutral pH to produce methane for 20d-is reported for the synchronous enhancement of methane production and reduction of H₂S production during AD. The experimental results showed that the cumulative methane yield was 861.2±6.1mL/g volatile solids (VS) of sludge pretreated at pH 10 in semi-continuous stirred anaerobic reactors for 84d, an increase of 49.6% over the yield in the control. Meanwhile, the cumulative production of H₂S was 144.1×10^-4mL/g VS, 54.2% lower than that in the control.

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.

How do Elevated CO2 and Nitrogen Addition Affect Functional Microbial Community Involved in Greenhouse Gas Flux in Salt Marsh System

Salt marshes are unique ecosystem of which a microbial community is expected to be affected by global climate change. In this study, by using T-RFLP analysis, quantitative PCR, and pyrosequencing, we comprehensively analyzed the microbial community structure responding to elevated CO₂ (eCO₂) and N addition in a salt marsh ecosystem subjected to CO₂ manipulation and N addition for about 3 years. We focused on the genes of microbes relevant to N-cycling (denitrification and nitrification), CH₄-flux (methanogens and methanotrophs), and S-cycling (sulfate reduction) considering that they are key functional groups involved in the nutrient cycle of salt marsh system. Overall, this study suggests that (1) eCO₂ and N addition affect functional microbial community involved in greenhouse gas flux in salt marsh system. Specifically, the denitrification process may be facilitated, while the methanogenesis may be impeded due to the outcompeting of sulfate reduction by eCO₂ and N. This implies that future global change may cause a probable change in GHGs flux and positive feedback to global climate change in salt marsh; (2) the effect of eCO₂ and N on functional group seems specific and to contrast with each other, but the effect of single factor would not be compromised but complemented by combination of two factors. (3) The response of functional groups to eCO₂ and/or N may be directly or indirectly related to the plant community and its response to eCO₂ and/or N. This study provides new insights into our understanding of functional microbial community responses to eCO₂ and/or N addition in a C3/C4 plant mixed salt marsh system.

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.

Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture

Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing

Root-associated microbial communities are very important for biogeochemical cycles in wetland ecosystems and help to elaborate the mechanisms of plant invasions. In the estuary of Jiulong River (China), Spartina alterniflora has widely invaded Kandelia obovata-dominated habitats, offering an opportunity to study the influence of root-associated bacteria. The community structures of endophytic and rhizosphere bacteria associated with selected plant species were investigated using the barcoded Illumina paired-end sequencing technique. The diversity indices of bacteria associated with the roots of S. alterniflora were higher than those of the transition stands and K. obovata monoculture. Using principal coordinate analysis with UniFrac metrics, the comparison of β-diversity showed that all samples could be significantly clustered into 3 major groups, according to the bacteria communities of origin. Four phyla, namely Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, were enriched in the rhizoplane of both salt marsh plants, while they shared higher abundances of Cyanobacteria and Proteobacteria among endophytic bacteria. Members of the phyla Spirochaetes and Chloroflexi were found among the endophytic bacteria of S. alterniflora and K. obovata, respectively. One of the interesting findings was that endophytes were more sensitive in response to plant invasion than were rhizosphere bacteria. With linear discriminate analysis, we found some predominant rhizoplane and endophytic bacteria, including Methylococcales, Pseudoalteromonadacea, Clostridium, Vibrio, and Desulfovibrio, which have the potential to affect the carbon, nitrogen, and sulfur cycles. Thus, the results provide clues to the isolation of functional bacteria and the effects of root-associated microbial groups on S. alterniflora invasions.