Effects of Spartina alterniflora Invasion on Soil Microbial Community Structure and Ecological Functions

Unraveling the impact of Spartina alterniflora invasion on greenhouse gas production and emissions in coastal saltmarshes: New insights from dissolved organic matter characteristics and surface-porewater interactions

Saltmarshes along the Chinese coast are threatened by the invasion of Spartina alterniflora (S. alterniflora). This study was carried out in the Andong Shoal, Hangzhou Bay, China, with the aim of comprehending the intricate impacts of S. alterniflora invasion on greenhouse gases (GHG) production and emissions. To address this issue, we thoroughly examined the chemistry of dissolved organic matter (DOM) and the rate of surface water-porewater interaction. Porewater and surface water samples were collected from farm land, S. alterniflora invaded areas, and Scirpus mariqueter (S. mariqueter) dominated areas. The findings indicated that the invasion of S. alterniflora impeded the interaction between surface water and porewater, resulting in reduced porewater exchange rates within its affected region (0.015-0.440 cm d-1), in contrast to areas dominated by S. mariqueter (9.635-18.232 cm d-1). The invasion also increased dissolved organic carbon concentration in porewater and created a stable and closed soil environment that resulted in DOM with smaller molecule sizes and higher humification levels. The presence of high tryptophan-like fluorescent DOM caused an increase in the production of methane and carbon dioxide in S. alterniflora invaded area. However, both limited surface-porewater exchange and significant differences in GHG concentrations between porewater and surface water suggested that the aerenchyma tissues of S. alterniflora may play an important role in transporting GHG from soil to the atmosphere.

Loss of microbial functional diversity following Spartina alterniflora invasion reduces the potential of carbon sequestration and nitrogen removal in mangrove sediments-from a gene perspective

Mangrove ecosystems play an important role in carbon (C) sequestration and nitrogen (N) removal. Although Spartina alterniflora has successively invaded native mangrove habitats during the preceding two decades, the effects of this invasion on the microbial functional potential involved in nutrient cycling remain unclear. In this study, metagenomic sequencing was used to investigate microbial C and N cycling in sediments derived from S. alterniflora and three native mangrove species (Kandelia obovata, Avicennia marina, and Aegiceras corniculatum). Greater differences in functional profiles of C and N cycling-related genes were observed between S. alterniflora and mangrove sediments than between different mangrove sediments. Functional diversity was lower in S. alterniflora sediments than in native mangrove sediments. The growth of Thaumarchaeota and Proteobacteria, was enhanced due to their resilience to diversity loss, while the growth of oligotrophs, such as Chloroflexi and Firmicutes, was inhibited in S. alterniflora sediments. Compared to mangrove sediments, the abundance of genes involved in C fixation and methane production was lower in S. alterniflora sediments. However, S. alterniflora significantly increased the gene abundance of pmo which controlled the oxidation process of CH4 to carbon dioxide. Additionally, genes involved in nitrification were enriched, whereas genes involved in N reduction processes, such as denitrification and dissimilatory nitrate reduction to ammonium, N immobilization, and N mineralization, were depleted in S. alterniflora sediments compared to mangrove sediments. Partial least squares regression models demonstrated that the decrease in soil organic C and increase in pH after S. alterniflora invasion induced the loss of microbial functional diversity, which was the main driver of changes in the abundances of genes involved in C and N cycling. Overall, our findings indicate that S. alterniflora invasion modifies the microbial functional profile of nutrient cycling in native mangrove ecosystems and potentially weakens the capacity of mangroves to sequester carbon and remove nitrogen.

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.

Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf

Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of "One Health."

Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve

Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.

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.

Seasonality and assembly of soil microbial communities in coastal salt marshes invaded by a perennial grass

Plant invasion profoundly changes the microbial-driven processes in the ecosystem; however, the seasonality of soil microbial communities and their assembly under plant invasion is poorly understood. In this study, coastal salt marshes with native Suaeda salsa (L.) Pall. and exotic Spartina alterniflora Loisel. in the Yellow River Estuary, North China, were selected, and soil bacterial and fungal communities and their seasonal variance were characterized by metabarcoding sequencing of the 16S rRNA gene and ITS2 regions, respectively. The importance of deterministic and stochastic processes in shaping bacterial and fungal seasonal assembly was explored by the null model. Results showed that soil microbes exhibited the lowest diversities in spring, while their diversity significantly improved in summer and autumn with the increase in organic carbon and nitrogen content in soils. Strong seasonal variances in microbial communities were observed, but plant invasion reduced the seasonal variation strength of soil bacteria. For the microbial assembly, the seasonal variability of soil bacterial community was mainly controlled by homogeneous selection, whereas soil fungal community was dominantly structured by stochastic processes. Among the selected variables, soil pH was the key abiotic factor driving the seasonal changes in bacteria and fungi. The microbial function annotation derived from taxonomy-based inference suggested that carbon metabolism was relatively stronger in spring, but nitrogen and sulfur metabolism increased evidently in summer and autumn, and the proportion of saprophytic fungi increased substantially after plant invasion. The seasonal turnover of bacterial and fungal groups were tightly associated with the seasonal variation in soil carbon and nitrogen contents. Collectively, these findings reveal the strong seasonal variability of different soil microbial constituents in plant-invaded coastal salt marshes and suggest the linkage between microbial community assembly and microbial-mediated functions in the context of plant invasions.

Nitrate Nitrogen and pH Correlate with Changes in Rhizosphere Microbial Community Assemblages during Invasion of Ambrosia artemisiifolia and Bidens pilosa

The rhizosphere of invasive plants presumably develops different soil microbial assemblages compared with native plants, which may hinder or promote their invasion. However, to date, no studies have clearly explored rhizosphere microbial community assemblages during invasion. The invasive species Ambrosia artemisiifolia L. and Bidens pilosa L. are widely distributed in China and are known to reduce local biodiversity and cause agricultural losses. Monoculture of A. artemisiifolia or B. pilosa, a mixture of each invasive and native species, and monoculture of native species were established to simulate different degrees of invasion. Metagenomic sequencing techniques were used to test microbial community structure and function. The aim was to explore the drivers of the assembly of peculiar functional microbes in the rhizosphere soil of invasive species during the long-term invasive-native species interaction. Compared with the native species, the relative abundance of 34 microbial genera was higher in the rhizosphere soil of the invasive species. The NO₃-N concentration in the rhizosphere soil from the A. artemisiifolia and B. pilosa monocultures was lower than that from monocultures of the three native plants, whereas pH followed the opposite trend. The NO₃-N concentration was significantly and negatively correlated with Sporichthya, Afipia, Actinokineospora, and Pseudolabrys. pH was positively correlated with Bradyrhizobium, Actinoplanes, Micromonospora, Steroidobacter, Burkholderia, and Labilithrix. The differences in soil microbes, NO₃-N concentrations, and pH between native and invasive species suggest that the rhizosphere soil microbial assemblages may vary. The reduced NO₃-N concentration and increased pH corelated with changes in rhizosphere microbial community during A. artemisiifolia and B. pilosa invasion. IMPORTANCE Soil microbial communities play a vital role in the growth of invasive plants. Invasive species may shape peculiar functional microbes in the rhizosphere soil of an invasive species to benefit its growth. However, the drivers of the assembly of soil microbial communities in the rhizosphere soil of invasive species remain unclear. Our study established the relationship between soil microbial communities and soil chemical properties during invasion by A. artemisiifolia and B. pilosa. Additionally, it showed that the presence of the invasive plants correlated with changes in NO₃-N and pH, as well as in rhizosphere microbial community assemblage. Furthermore, the study provided important insights into the difference in the microbial community assembly between native and invasive plant species.

Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

The Effects of Secondary Growth of Spartina alterniflora after Treatment on Sediment Microorganisms in the Yellow River Delta

As a typical invasive species, Spartina alterniflora is widely recognized as one of the primary threats to biodiversity in various habitats, including wetlands. Although the invasion by S. alterniflora has been managed in multiple ways, it may reappear after treatment. How S. alterniflora affects the soil microbial community in coastal wetlands during its regeneration process has not yet been clarified. Here, rhizosphere soil samples (RSPs) and bulk soil samples (SSPs) were collected in the S. alterniflora community and a high-throughput sequencing method was conducted to analyze the composition and diversity of soil microorganisms. Meanwhile, we also obtain the soil physicochemical properties. In the present study, there was no significant difference in the alpha diversity of both bacterial and fungal communities in the SSP and RSP groups. The PCoA (principal coordinate analysis) also showed that the microbial community structure did not differ significantly between the SSP and RSP groups. The results showed that except for pH, the total sulfur (TS) content, total nitrogen (TN) content, and electrical conductivity (EC) did not differ significantly (p > 0.05) between the SSP and RSP groups. The composition of the bacterial and fungal community in the rhizosphere of S. alterniflora was similar to that found in the surrounding soils. The top two dominant bacterial phyla were Proteobacteria and Desulfobacterota in the present study. Venn diagram results also support this view; most OTUs belong to the common OTUs of the two groups, and the proportion of unique OTUs is relatively small. The LEfSe (LDA effect size) analysis showed that Campylobacterota (at the phylum level) and Sulfurimonas (at the genus level) significantly increased in the RSP group, implying that the increased Sulfurimonas might play an essential role in the invasion by S. alterniflora during the under-water period. Overall, these results suggest that the bacterial and fungal communities were not significantly affected by the S. alterniflora invasion due to the short invasion time.

Application of Organic Fertilizer Changes the Rhizosphere Microbial Communities of a Gramineous Grass on Qinghai–Tibet Plateau

The effects of organic fertilizer application on the soil microbial community in grassland systems have been extensively studied. However, the effects of organic fertilizers on the structure of rhizosphere microbial communities are still limited. In this study, the diversity and composition of rhizosphere microbial communities of a gramineous grass Elymus nutans under organic fertilizer treatment were studied in an artificial pasture on Qinghai–Tibet Plateau. After a growing season, the application of organic fertilizer not only increased the height and biomass of Elymus nutans, but also changed the rhizosphere microbial compositions. In particular, organic fertilizer increased the diversity of rhizosphere bacterial community and inhibited the growth of pathogenic bacteria such as Acinetobacter, but the opposite trend was observed for the diversity of fungal community. The assembly process of fungal community was changed from a stochastic process to a deterministic process, indicating that selection was strengthened. Additionally, both the infection rate of arbuscular mycorrhizal fungi (AMF) toward host plants and the development of AMF-related structures were significantly increased after the application of organic fertilizer. Our study demonstrated that the addition of organic fertilizer to artificial pasture could improve the growth of grass through the alteration of the rhizosphere microbial communities. Organic fertilizer had a greater selectivity for the bacterial and the fungal communities that enhanced the niche filtration in this community, further benefiting the yield of forages.

Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem

This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora .

Diversity and Potential Function of Prokaryotic and Eukaryotic Communities from Different Mangrove Sediments

Mangrove trees generally play important roles in protecting intertidal ecosystems. The mangrove root-associated sediments provide a repertoire of microbial communities that contribute to pivotal ecological functions in the system. In the present study, we used the high-throughput sequencing and PICRUSt-predicted functional information (based on 16S/18S rDNA profiles) to investigate the bacterial, archaeal, and fungal communities in two mangrove systems, located in the estuary of the Jiulong River (China), with different contaminated conditions and frequencies of human activity. Diverse distribution patterns for microbial communities were observed in six sediment samples collected from the two survey areas, which were found to be related mainly to the substrates in mangrove sediments. The sediments were predominated by relatively higher ratios of heterotrophic bacteria that participated in the degradation of organic matters, including phylum of Chloroflexi, Acidobacteriota, Desulfobacterota, and Proteobacteria. In addition, Crenarchaeota and Ascomycota presented the highest abundances of archaea and fungi, respectively. The relatively high concentrations of calcium, nitrogen, magnesium, and phosphorus in mangrove sediments correlated significantly with the microbial communities. In addition, although the potential functions were similar in the two sites based on COG and KEGG pathways, the abundances of enzymes involved in the degradation processes of cellulose and hemicellulose and the metabolism of nitrogen and sulfur presented distinctions. These results provide insights into the environmental conditions shaping microbial assemblies of the mangrove sediments under the impacts of human activities; for instance, a more abundant amount of calcium was found in urban areas in this study.

Effect of land-use and land-cover change on mangrove soil carbon fraction and metal pollution risk in Zhangjiang Estuary, China

Land-use and land-cover change (LULCC) is the main cause of mangrove deforestation and degradation. However, the effect of LULCC on mangrove soil organic carbon (SOC) fractions and metal pollution risks, and the difference between the effects of those two soil evolutions are largely unknown. Here, we collected soil samples from natural systems (mangroves and mudflat), land-cover changes (Spartina alterniflora invasion), and anthropogenic land-use changes (cropland and culture pond) in Zhangjiang Estuary. We determined the soil aggregate fractions (macro-aggregate, micro-aggregate, and silt-clay fraction) and the associated carbon, and heavy metal dynamics. Our findings suggested that LULCC did not remarkably affect SOC contents, but changed the soil aggregate structures. LULCC significantly increased aggregate-associated carbon fractions, especially macro-aggregate carbon fraction. The large proportion of silt-clay fraction in natural systems was corresponding to a high percentage of mineral organic carbon, indicating that LULCC decreases the mangrove SOC stability. Land-cover change promoted the accumulation of SOC, nitrogen, and heavy metals compared with uninvaded mudflat. The heavy metal contents in mangrove soil were highest among all studied soils, expect for Cd, which suggested that mangrove soil had high metal accumulation. However, land-use changes could stimulate the mobility and dynamics of metals enriched in mangrove soils; these changes, especially in cropland, will also cause a large amount of exogenous Cd being exported into the adjacent aquatic environment. Thus, mangrove shifts metal pollutant from sink to source when affected by land-use changes. The contamination index demonstrated that heavy metals have posed ecological risks, especially for Cd in cropland. Compared with mangrove, land-use change was dominated by single-element pollution, but land-cover change showed low multiple-element complex pollution. These findings elucidate the effects of LULCC on mangrove SOC fraction and metal pollution risk, and are of great significance for designing the long-term management and conservation policies for mangrove managers.