Changes in sediment bacterial community in response to long-term nutrient enrichment in a subtropical seagrass-dominated estuary

Insight into the bacterial communities in the sediment-water interface across different salinities of Pacific White shrimp, Penaeus vannamei, by metabarcoding

Microbes play an important role in the food chain by metabolizing organic matter, cycling nutrients, and maintaining a dynamic equilibrium among organisms in water and sediment. The objective is to study the fluctuating taxonomic microbial diversity profile in the sediment-water interface at different days of culture (DOC) of Penaeus vannamei in varying salinities using the Illumina MiSeq platform. Sediment samples were collected in Tamil Nadu, India, from low-saline, brackish water, and high-saline ponds at 30, 60, and 90 DOC. Bacterial richness and diversity in species were high in low-saline ponds. Beta-diversity variation indicated more differences in bacterial composition in high- and low-saline ponds. The predominant phyla observed were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, and Cyanobacteria. High-saline ponds accounted for more nitrification bacterial communities, sulfur-reducing bacterial communities, sulfur-oxidizing bacterial communities, and high redox potential, whereas denitrification bacterial communities were high in brackish water ponds.

Functional effects of subsidies and stressors on benthic microbial communities along freshwater to marine gradients

Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater-to-marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter.

Sulfide-carbonate-mineralized functional bacterial consortium for cadmium removal in flue gas

Sulfide-carbonate-mineralized functional bacterial consortium was constructed for flue gas cadmium biomineralization. A membrane biofilm reactor (MBfR) using the bacterial consortium containing sulfate reducing bacteria (SRB) and denitrifying bacteria (DNB) was investigated for flue gas cadmium (Cd) removal. Cadmium removal efficiency achieved 90%. The bacterial consortium containing Citrobacter, Desulfocurvus and Stappia were dominated for cadmium resistance-nitrate-sulfate reduction. Under flue gas cadmium stress, ten cadmium resistance genes (czcA, czcB, czcC, czcD, cadA, cadB, cadC, cueR, copZ, zntA), and seven genes related to sulfate reduction, increased in abundance; whereas others, nine genes related to denitrification, decreased, indicating that cadmium stress was advantageous to sulfate reduction in the competition with denitrification. A bacterial consortium could capable of simultaneously cadmium resistance, sulfate reduction and denitrification. Microbial induced carbonate precipitation (MICP) and biological adsorption process would gradually yield to sulfide-mineralized process. Flue gas cadmium could transform to Cd-EPS, cadmium carbonate (CdCO3) and cadmium sulfide (CdS) bioprecipitate. The functional bacterial consortium was an efficient and eco-friendly bifunctional bacterial consortium for sulfide-carbonate-mineralized of cadmium. This provides a green and low-carbon advanced treatment technology using sulfide-carbonate-mineralized functional bacterial consortium for the removal of cadmium or other hazardous heavy metal contaminants in flue gas.

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil

The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.

Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes

Seagrasses are vital coastal ecosystem engineers, which are mutualistically associated with microbial communities that contribute to the ecosystem services provided by meadows. The seagrass microbiome and sediment microbiota play vital roles in belowground biogeochemical and carbon cycling. These activities are influenced by nutrient, carbon and oxygen availability, all of which are modulated by environmental factors and plant physiology. Seagrass meadows are increasingly threatened by nutrient pollution, and it is unknown how the seagrass microbiome will respond to this stressor. We investigated the effects of fertilization on the physiology, morphology and microbiome of eelgrass (Zostera marina) cultivated over 4 weeks in mesocosms. We analyzed the community structure associated with eelgrass leaf, root and rhizosphere microbiomes, and of communities from water column and bulk sediment using 16S rRNA amplicon sequencing. Fertilization led to a higher number of leaves compared with that of eelgrass kept under ambient conditions. Additionally, fertilization led to enrichment of sulfur and nitrogen bacteria in belowground communities. These results suggest nutrient enrichment can stimulate belowground biogeochemical cycling, potentially exacerbating sulfide toxicity in sediments and decreasing future carbon sequestration stocks.

Bacterial community composition in soils covered by different vegetation types in the Yancheng tidal marsh

Coastal wetland vegetation plays an important role in maintaining ecological function and is a key factor affecting the soil bacterial community. Spartina alterniflora was introduced to the Yancheng tidal marsh to stabilize the sediments and gradually replaced the native plants. However, the changes in the soil bacterial community profile caused by S. alterniflora invasion are poorly characterized. Here, we used MiSeq sequencing to compare the composition of the bacterial community in soil at different depths under exotic S. alterniflora (SA), native Phragmites australis (PA), and native Suaeda salsa (SS). The results showed that the pH value was lower, but the salinity, soil organic carbon, total nitrogen, and number of 16S rRNA genes were higher in SA soils than in PA and SS soils. Overall, Proteobacteria was the dominant bacterial phylum, followed by Chloroflexi, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Nitrospirae. Anaerolineae in the Chloroflexi phylum showed the greatest difference based on vegetation, accounting for 14.4% of the overall bacterial community in SA soils but only about 3.8% of those in PA and SS soils. The composition, interaction, and predicted functional profiles of the bacterial community in SA soils were significantly different from those in PA and SS soils, especially for functions related to the sulfur and nitrogen cycles. Salinity was negatively correlated with the Shannon index and accounted for 37.7% of the total variation in the bacterial community, making it the most important environmental factor. Our results showed the differences in bacterial community composition among different vegetation types and soil depths in the Yancheng tidal marsh, which provides a microbial basis for a better understanding of the ecological functions in this ecosystem.

Nutrients and heavy metals mediate the distribution of microbial community in the marine sediments of the Bohai Sea, China

The Bohai Sea, one of the largest marginal seas in China, is extensively influenced by human and industrial activities. The pollutant loads from anthropogenic activities have induced severe ecological problems. The study investigates the physicochemical characteristics of seawater and sediments in Bohai Bay and Laizhou Bay of the Bohai Sea. The diversity and composition of microbial community in sediments are analyzed by 16S rRNA gene amplicon sequencing. The sequencing results present 16 phyla and 31 classes from the samples. Proteobacteria constituted a dominant phylum, of which the classes of Gamma-, Delta-, and Epsilon-are predominant sub-divisions. Nitrogen, phosphorus, and sulfur cycling related microbes present high abundance in both bays. The metabolism of organic matters is the main factor that influences the distribution of microbial communities in Bohai Bay, while the inflow of Yellow River is the dominant factor that influences the distribution of microbial communities in Laizhou Bay. Sulfur oxidizing process is expected to be positively influenced by heavy metals, while ammonia (NH₄⁺) oxidizing process is prone to be negatively affected by heavy metals in both bays. Microbial communities in the offshore sediments of Laizhou Bay and the majority microbial communities in Bohai Bay sediments are subject to similar predominant controlling factors. This phenomenon is likely ascribed to ocean circulation. The results of this study can provide constructive guidelines on ecosystem management of marginal seas in Bohai and elsewhere.

The effect of cations (Na+, Mg2+, and Ca2+) on the activity and structure of nitrifying and denitrifying bacterial communities

Wastewaters generated in regions with water scarcity usually have high alkalinity, hardness, and elevated osmotic pressure (OP). Those characteristics should be considered when using biological systems for wastewater treatment along with the salinity heterogeneity. The interaction of different salts in mixed electrolyte solutions may cause inhibition, antagonism, synergism, and stimulation effects on microbial communities. Little is known about those effects on microbial activity and community structure of nitrifying and denitrifying bacteria. In this work, factorial design was used to evaluate the effects of NaCl, MgCl₂ and CaCl₂ on nitrifying and denitrifying communities. Antagonistic relationships between all salts were observed and they had greater magnitude on the nitrifying community. Stimulus and synernism were more evident on the nitrifying and denitrifying experiments, respectively. For this reason, the highest nitrification and denitrification specific rates were 1.1 × 10^-1 mgN-NH₄⁺ gSSV^-1 min^-1 for condition 01 and 6.5 × 10^-2 mgN-NO₃^- gSSV^-1 min^-1 for control condition, respectively. The toxicity of the salts followed the order of NaCl > MgCl₂ > CaCl₂ and the antagonism between MgCl₂ and NaCl was the most significant. PCR/DGGE analyses showed that Mg²⁺ may be the element that expresses the least influence in the differentiation of microbial structure even though it significantly affects the activity of the autotrophic microorganisms. The same behavior was observed for Ca²⁺ on denitrifying microorganism. In addition, microbial diversity and richness was not negatively affected by different salinities. Genetic sequencing suggested that the genus Aeromonas, Alishewanella, Azospirillum, Pseudoalteromonas, and Thioalkalivibrio were outstanding on ammonium and nitrate removal under saline conditions. The specific toxicity of each salt and the interactions among them are the major effects on microbial activity in biological wastewater treatments rather than the osmotic pressure caused by the final salinity.

Spartina alterniflora invasion alters soil bacterial communities and enhances soil N2O emissions by stimulating soil denitrification in mangrove wetland

Chinese mangrove, an important ecosystem in coastal wetlands, is sensitive to the invasive alien species Spartina alterniflora. However, the effects of the S. alterniflora invasion on mangrove soil N₂O emissions and the underlying mechanisms by which emissions are affected have not been well studied. In this study, the N₂O emitted from soils dominated by two typical native mangroves (i.e. Kandelia obovata: KO; Avicennia marina: AM), one invaded by S. alterniflora (SA), and one bare mudflat (Mud) were monitored at Zhangjiang Mangrove Estuary (where S. alterniflora is exotic). Together with soil biogeochemical properties, the potential denitrification rate and the composition of soil bacterial communities were determined simultaneously by ¹⁵NO₃^- tracer and high-throughput sequencing techniques, respectively. Our results showed that S. alterniflora invasion significantly (p < 0.05) increases soil N₂O emissions by 15-28-fold. In addition, isotope results revealed that the soil potential denitrification rate was significantly (p < 0.05) enhanced after S. alterniflora invasion. Moreover, the S. alterniflora invasion significantly (p < 0.05) decreased soil bacterial α-diversity and strongly modified soil bacterial communities. Indicator groups strongly associated with S. alterniflora were Chloroflexia, Alphaproteobacteria, and Bacilli, each of which was abundant and acts as connector in the co-occurrence network. FAPROTAX analysis implied that the S. alterniflora invasion stimulated soil denitrification and nitrification while depressing anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA). Redundancy analysis (RDA) found that soil organic matter (SOM) and pH were the most important environmental factors in altering soil bacterial communities. Taken together, our results imply that the S. alterniflora invasion in mangrove wetlands significantly stimulates soil denitrification and N₂O emissions, thereby contributing N₂O to the atmosphere and contributing to global climate change.

Seaweed Loads Cause Stronger Bacterial Community Shifts in Coastal Lagoon Sediments Than Nutrient Loads

The input of nutrients from anthropogenic sources is the leading cause of coastal eutrophication and is usually coupled with algal/seaweed blooms. Effects may be magnified in semi-enclosed systems, such as highly productive coastal lagoon ecosystems. Eutrophication and seaweed blooms can lead to ecosystem disruption. Previous studies have considered only one of these factors, disregarding possible interactive effects and the effect of the blooming species' identity on sediment bacterial communities. We tested the effect of experimental nutrient loading and two common blooming seaweeds (Ulva rigida and Gracilaria vermiculophylla) in coastal lagoon sediments, on the structure of bacterial communities (using 16S rRNA amplicon sequencing) and corresponding putative functional potential (using PiCRUSt). At the Operational Taxonomic Unit (OTU) level, the addition of nutrients reduced bacterial community α-diversity and decreased the abundance of sulfate reducers (Desulfobacterales) compared to sulfur oxidizers/denitrifiers (Chromatiales and Campylobacterales), whereas this was not the case at the order level. Seaweed addition did not change bacterial α-diversity and the effect on community structure depended on the taxonomic level considered. The addition of Gracilaria increased the abundance of orders and OTUs involved in sulfate reduction and organic matter decomposition (Desulfobacterales, Bacteroidales, and Clostridiales, respectively), an effect which was also detected when only Ulva was added. Nutrients and the seaweeds combined only interacted for Ulva and nutrients, which increased known sulfide oxidizers and denitrifiers (order Campylobacterales). Seaweed enrichment affected putative functional profiles; a stronger increase of sulfur cycling KEGG pathways was assigned to nutrient-disturbed sediments, particularly with the seaweeds and especially Ulva. In contrast, nitrogen and sulfur cycle pathways showed a higher abundance of genes related to dissimilatory nitrate reduction to ammonium (DNRA) in Ulva+nutrients treatments. However, the other seaweed treatments increased the nitrogen fixation genes. Thiosulfate reduction, performed by sulfate-reducing bacteria, increased in seaweed treatments except when Ulva was combined with nutrients. In conclusion, the in situ addition of nutrients and the seaweeds to intertidal sediments affected the bacterial communities differently and independently. The predicted functional profile suggests a shift in relative abundances of putative pathways for nitrogen and sulfur cycles, in line with the taxonomic changes of the bacterial communities.

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows

Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH₄⁺ and PO₄³⁻ content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.

In situ soft sediment nutrient enrichment: A unified approach to eutrophication field experiments

Adding fertiliser to sediments is an established way of studying the effects of eutrophication but a lack of consistent methodology, reporting on enrichment levels, or guidance on application rates precludes rigorous synthesis and meta-analysis. We developed a simple enrichment technique then applied it to 28 sites across an intertidal sandflat. Fertiliser application rates of 150 and 600gNm(-2) resulted in pore water ammonium concentrations respectively 1-110 and 4-580×ambient, with greater elevations observed in deeper (5-7cm) than surface (0-2cm) sediments. These enrichment levels were similar to eutrophic estuaries and were maintained for at least seven weeks. The high between-site variability could be partially explained by the sedimentary environment and macrofaunal community (42%), but only at the high application rate. We suggest future enrichment studies should be conducted in situ across large environmental gradients to incorporate real world complexity and increase generality of conclusions.

Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea

Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species' capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.

Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing

The changes of microbial community in aquaculture systems under the effects of stocking densities and seasonality were investigated in tilapia ponds. Total DNAs were extracted from the water samples, 16S rRNA gene was amplified and the bacterial community analyzed by Illumina high-throughput sequencing obtaining 3486 OTUs, from a total read of 715,842 sequences. Basing on the analysis of bacterial compositions, richness, diversity, bacterial 16S rRNA gene abundance, water sample comparisons and existence of specific bacterial taxa within three fish ponds in a 4 months period, the study conclusively observed that the dominant phylum in all water samples were similar, and they included; Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes and Chlorobi, distributed in different proportions in the different months and ponds. The seasonal changes had a more pronounced effect on the bacterioplankton community than the stocking densities; however some differences between the ponds were more likely caused by feed coefficient than by stocking densities. At the same time, most bacterial communities were affected by the nutrient input except phylum Cyanobacteria that was also affected by the feed control of tilapia.