Detection of sentinel bacteria in mangrove sediments contaminated with heavy metals

Eco-resilience of China's mangrove wetlands: The impact of heavy metal pollution and dynamics

Mangrove forests in China have significantly degraded over the past several decades primarily due to rapid economic growth and land reclamation for aquaculture and infrastructure development. Among various threats, heavy metal pollution, primarily from urbanization, agricultural runoff, and industrial runoff, poses a substantial risk to mangroves in China. It impairs their ecological functions, limiting biodiversity and reducing their natural ability to sequester carbon and detoxify coastal areas. Despite these challenges, the mangrove ecosystem's resilience in China has not been completely compromised. Natural adaptations and phytoremediation mechanisms, such as limiting metal uptake, excreting metal binding proteins, upregulating antioxidants, forming Fe plague, excreting metals through salt glands, and tolerance to specific metal concentrations, help mitigate heavy metal toxicity. However, these adaptive strategies are limited by the extent of pollutants and the speed at which these pollution factors arise. This review highlights a need to shift restoration efforts from expanding mangrove areas to enhancing ecosystem integrity, with a specific focus on reducing heavy metal pollution through phytoremediation. It also examines how heavy metal interactions at the sediment-water interface impact microbial communities and local fauna, contributing to climate change. Addressing these challenges is critical to improving mangrove conservation in China and ensuring the long-term health and resilience of these critical ecosystems for future generations.

Simulation of organic acid migration and transformation in Mangrove soils based on soil column experiments

The practice of directly applying unfermented and decomposed organic matter to plants is rare in the growth process of terrestrial plants. The organic matter content at the discharge outlet of shrimp ponds is usually high. Therefore, it is necessary to collect soil from the discharge outlet of shrimp ponds and simulate the migration and transformation pathways of organic acids and related metabolic microorganisms in soil of mangrove wetlands through laboratory soil columns and the HYDRUS-1D model. Results showed that the content of oxalic acid remained relatively stable in the soil column at different depths, citric acid settled downward along the vertical direction, the concentration of acetic acid in the depth range of 30-50 cm increased. The organic acids formed insoluble or slightly soluble precipitates in the form of organic acid calcium, the organic acids in 40-50 cm were completely neutralized on the 18th day. The abundance of acid-producing Acinetobacter Johnsonii increased during the later stages of anaerobic acidification and disappeared after the addition of Ca(OH)2. The results of HYDRUS-1D simulation showed that the adsorption, deposition and transport of organic acids in the mangrove wetland were poor, the results of vertical infiltration modelling were in agreement with the soil column experiments.

Genome mining and metabolite profiling illuminate the taxonomy status and the cytotoxic activity of a mangrove-derived Microbacterium alkaliflavum sp. nov

The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a mangrove sediment-derived strain B2969T was identified as a novel type strain within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the validly named species of the genus. The type strain B2969T (= MCCC 1K099113T = JCM 36707 T) is proposed to represent Microbacterium alkaliflavum sp. nov.. The crude extracts of strain B2969T showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC50 values of ranging from 3.5 µg/µL to 2.4 µg/µL respectively. Genome analysis of strain B2969T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including cytotoxic compounds desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC-MS/MS)-based molecular networking strategy led to the identification of 10 compounds with potent cytotoxic activity in ethyl acetate extracts of strain B2969T. Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC-MS/MS analysis revealed its ability to produce bioactive compounds.BackgroundMangrove ecosystems are largely unexplored sources of Actinomycetota, which represent potential important reservoirs of bioactive compounds. The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a novel species, namely B2969T, within the genus Microbacterium that showed cytotoxicity against nasopharyngeal carcinoma (NPC) cell lines was isolated from mangrove sediments. Genome mining and metabolic profiling analyses were explored here to assess its biosynthetic potential of metabolites with cytotoxic properties.ResultsHere, a mangrove sediment-derived strain B2969T was identified as a novel species within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99.0%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the type strains of this genus. We proposed that strain B2969T represents a new species, in which the name Microbacterium alkaliflavum sp. nov. is proposed. The strain showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC50 values of ranging from 3.512 µg/µL to 2.428 µg/µL respectively. Genome analysis of strain B2969T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC-MS/MS)-based molecular networking strategy led to the identification of 10 potent cytotoxic compounds in ethyl acetate extracts of strain B2969T.ConclusionsThis study confirmed the taxonomy status of type strain B2969T (= MCCC 1K099113T = JCM 36707 T) within the genus Microbacterium, in which the name Microbacterium alkaliflavum sp. nov.. Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC-MS/MS analysis revealed its ability to produce bioactive substances, providing sufficient evidence for the potential of Microbacterium species in the discovery of novel pharmaceuticals.

S0-dependent bio-reduction for antimonate detoxification from wastewater by an autotrophic bioreactor with internal recirculation

Elemental sulfur (S0) autotrophic reduction is a promising approach for antimonate [Sb(V)] removal from water; however, it is hard to achieve effective removal of total antimony (TSb). This study established internal recirculation in an S0 autotrophic bioreactor (SABIR) to enhance TSb removal from Sb(V)-contaminated water. Complete Sb(V) reduction (10 mg/L) with bare residual Sb(III) (< 0.26 mg/L) was achieved at hydraulic retention time (HRT) = 8 h. Shortening HRT adversely affected the removal efficiencies of Sb(V) and TSb; meanwhile, an increased reflux ratio was conducive to Sb(V) and TSb removal at the same HRT. Sulfur disproportionation occurred in the SABIR and was the primary source for SO42- generation and alkalinity consumption. The alkalinity consumption decreased with the shortening HRT and increased with an increased reflux ratio at the same HRT. The generated SO42- was significantly higher (50-100 times) than the theoretical value for Sb(V) reduction. Coefficient of variation (CV), first-order kinetic models, and osmolality analyses showed that internal recirculation did not significantly affect the stability of SABIR but contributed to enhancing TSb removal by increasing mass transfer and reflowing generated sulfide back to the SABIR. SEM-EDS, Raman spectroscopy, XRD and XPS analyses identified that the precipitates in the SABIR were Sb2S3 and Sb-S compounds. In addition, high-throughput sequencing analysis revealed the microbial community structure's temporal and spatial distribution in the SABIR. Dominant genera, including unclassified-Proteobacteria (18.72-38.99%), Thiomonas (0.94-4.87%) and Desulfitobacterium (1.18-2.75%) might be responsible for Sb(V) bio-reduction and removal. This study provides a strategy to remove Sb from water effectively and supports the theoretical basis for the practical application of the SABIR in Sb(V)-contaminated wastewater.

Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea

Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.

Effects of microplastics on microbial community structure and wheatgrass traits in Pb-contaminated riparian sediments under flood-drainage-planting conditions

The coexistence of microplastics (MPs) and heavy metals in sediments has caused a potential threat to sediment biota. However, differences in the effects of MPs and heavy metals on microbes and plants in sediments under different sediment conditions remain unclear. Hence, we investigated the influence of polyethylene (PE) and polylactic acid (PLA) MPs on microbial community structure, Pb bioavailability, and wheatgrass traits under sequential incubation of sediments (i.e., flood, drainage, and planting stages). Results showed that the sediment enzyme activities presented a dose-dependent effect of MPs. Besides, 10 % PLA MPs significantly increased the F1 fractions in three stages by 11.13 %, 30.10 %, and 17.26 %, respectively, thus resulting in higher Pb mobility and biotoxicity. MPs altered sediment bacterial composition and structures, and bacterial community differences were evident in different incubation stages. Moreover, the co-exposure of PLA MPs and Pb significantly decreased the shoot length and total biomass of wheatgrass and correspondingly activated the antioxidant enzyme activity. Further correlation analysis demonstrated that community structure induced by MPs was mainly driven by sediment enzyme activity. This study contributes to elucidating the combined effects of MPs and heavy metals on sediment ecosystems under different sediment conditions.

Advanced sustainable processes via functionalized Fe-N co-doped fishbone biochar for the remediation of plasticizer di-(2-ethylhexyl) phthalate-contaminated marine sediment

Sediments are important sinks for di-(2-ethylhexyl) phthalate (DEHP), a plasticizer, and thus, maintaining the sediment quality is essential for eliminating plasticizers in aqueous environments and recovering the sediment ecological functions. To mitigate the potential risks of endocrine-disrupting compounds, identifying an effective and eco-friendly degradation process of organic pollutants from sediments is important. However, sustainable and efficient utilization of slow pyrolysis for converting shark fishbone to generate shark fishbone biochar (SFBC) has rarely been explored. Herein, SFBC biomass was firstly produced by externally incorporating heteroatoms or iron oxide onto its surface in conjunction with peroxymonosulfate (PMS) to promote DEHP degradation and explore the associated benthic bacterial community composition from the sediment in the water column using the Fe-N-SFBC/PMS system. SFBC was pyrolyzed at 300-900 °C in aqueous sediment using a carbon-advanced oxidation process (CAOP) system based on PMS. SFBC was rationally modified via N or Fe-N doping as a radical precursor in the presence of PMS (1 × 10-5 M) for DEHP removal. The innovative SFBC/PMS, N-SFBC/PMS, and Fe-N-SFBC/PMS systems could remove 82%, 65%, and 90% of the DEHP at pH 3 in 60 min, respectively. The functionalized Fe3O4 and heteroatom (N) co-doped SFBC composite catalysts within a hydroxyapatite-based structure demonstrated the efficient action of PMS compared to pristine SFBC, which was attributed to its synergistic behavior, generating reactive radicals (SO4•-, HO•, and O2•-) and non-radicals (1O2) involved in DEHP decontamination. DEHP was significantly removed using the combined Fe-N-SFBC/PMS system, revealing that indigenous benthic microorganisms enhance their performance in DEHP-containing sediments. Further, DEHP-induced perturbation was particularly related to the Proteobacteria phylum, whereas Sulfurovum genus and Sulfurovum lithotrophicum species were observed. This study presents a sustainable method for practical, green marine sediment remediation via PMS-CAOP-induced processes using a novel Fe-N-SFBC composite material and biodegradation synergy.

Bioponic systems with biochar: Insights into nutrient recovery, heavy metal reduction, and microbial interactions in digestate-based bioponics

Bioponics is a nutrient-recovery technology that transforms nutrient-rich organic waste into plant biomass/bioproducts. Integrating biochar with digestate from anaerobic wastewater treatment process can improve resource recovery while mitigating heavy metal contamination. The overarching goal of this study was to investigate the application of biochar in digestate-based bioponics, focusing on its efficacy in nutrient recovery and heavy metal removal, while also exploring the microbial community dynamics. In this study, biochar was applied at 50 % w/w with 500 g dry weight of digestate during two 28-day crop cycles (uncontrolled pH and pH 5.5) using white stem pak choi (Brassica rapa var. chinensis) as a model crop. The results showed that the digestate provided sufficient phosphorus and nitrogen, supporting plant growth. Biochar amendment improved plant yield and phosphate solubilization and reduced nitrogen loss, especially at the pH 5.5. Furthermore, biochar reduced the heavy metal accumulation in plants, while concentrating these metals in the residual sludge. However, owing to potential non-carcinogenic and carcinogenic health risks, it is still not recommended to directly consume plants cultivated in digestate-based bioponic systems. Additionally, biochar amendment exhibited pronounced impact on the microbial community, promoting microbes responsible for nutrient solubilization and cycling (e.g., Tetrasphaera, Herpetosiphon, Hyphomicrobium, and Pseudorhodoplanes) and heavy metal stabilization (e.g., Leptolinea, Fonticella, Romboutsia, and Desulfurispora) in both the residual sludge and plants. Overall, the addition of biochar enhanced the microbial community and facilitated the metal stabilization and the cycling of nutrients within both residual sludge and root systems, thereby improving the overall efficiency of the bioponics.

Physiological characteristics, rhizosphere soil properties, and root-related microbial communities of Trifolium repens L. in response to Pb toxicity

Trifolium repens L. (T. repens) is considered a potential phytoremediation species due to its large biomass and ability to accumulate and tolerate heavy metals. Lead (Pb) is an important heavy metal pollutant that can affect plant growth, photosynthesis, and enzyme activity. However, response mechanism of microorganisms in three root niches of metal tolerant plants to Pb is not completely understood. Therefore, in this study, a Pb poisoning model of T. repens was established with a Pb gradient (0, 1000 mg/kg, 2000 mg/kg, and 3000 mg/kg), and was used to evaluate growth and physiological responses, as well as enrichment and transport coefficients in T. repens, and explore the characteristics of rhizosphere soil and microbial composition of three root niches. We found that Pb stress caused oxidative injury, and inhibited photosynthesis in T. repens. 16S rDNA sequencing analysis showed that the richness of microbial communities in bulk soil was higher than that in rhizosphere soil both under Pb stress and Pb nonstress conditions. Moreover, Proteobacteria was dominant phylum in bulk and rhizosphere soils, and Proteobacteria and Cyanobacteria were dominant phylum in endophytic bacteria. For the first time, we systematically investigated the response of Pb from bulk soil to plant leaves. The results showed that microbial interaction existed between bulk and rhizosphere soil. Rhizosphere bacterium Haliangium was positively correlated with urease activity and soil nutrients. Endophytic bacterium Pseudomonas was positively correlated with plant biomass and played an important role in Pb tolerance of T. repens. In addition, endophytic bacteria formed complex correlation networks with growth and physiological indexes of both root and shoot, moreover the network in root was more complicated. Taken together, Pb stress dose-dependently inhibited the growth of plants. This study provided a theoretical basis for the further development of microbial cooperation with plant remediation of heavy metal contaminated soil.

Effects of plastic contamination on carbon fluxes in a subtropical coastal wetland of East China

Coastal wetlands are recognized as carbon sinks that play an important role in mitigating global climate change because of the strong carbon uptake by vegetation and high carbon sequestration in the soil. Over the last few decades, plastic waste pollution in coastal zones has become increasingly serious owing to high-intensity anthropogenic activities. However, the influence of plastic waste (including foam waste) accumulation in coastal wetlands on carbon flux remains unclear. In the Yangtze Estuary, we investigated the variabilities of vegetation growth, carbon dioxide (CO2) and methane (CH4) fluxes, and soil properties in a clean Phragmites australis marsh and mudflat and a plastic-polluted marsh during summer and autumn. The clean marsh showed a strong CO2 uptake capacity (a carbon sink), and the clean mudflat showed a weak CO2 sink during the measurement period. However, polluted marshes are a significant source of CO2 emissions. Regardless of the season, the gross primary production and vegetation biomass of the polluted marshes were on average 9.5 and 1.1 times lower than those in the clean marshes, respectively. Ecosystem respiration and CH4 emissions in polluted marshes were significantly higher than those in clean marshes and mudflats. Generally, the soil bulk density and salinity in polluted marshes were lower, whereas the median particle size was higher at the polluted sites than at the clean sites. Increased soil porosity and decreased salinity may favor CO2 and CH4 emissions through gas diffusion pathways and microbiological behavior. Moreover, the concentrations of heavy metals in the soil of plastic-polluted marshes were 1.24-1.49 times higher than those in the clean marshes, which probably limited vegetation growth and CO2 uptake. Our study highlights the adverse effects of plastic pollution on the carbon sink functions of coastal ecosystems, which should receive global attention in coastal environmental management.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.

An eco-sustainable approach towards heavy metals remediation by mangroves from the coastal environment: A critical review

Mangroves provide various ecosystem services, carbon sequestration, biodiversity depository, and livelihoods. They are most abundant in marine and coastal ecosystems and are threatened by toxic contaminants like heavy metals released from various anthropogenic activities. However, they have significant potential to survive in salt-driven environments and accumulate various pollutants. The adverse effects of heavy metals have been extensively studied and recognized as toxic to mangrove species. This study sheds light on the dynamics of heavy metal levels, their absorption, accumulation and transport in the soil environment in a mangrove ecosystem. The article also focuses on the potential of mangrove species to remove heavy metals from marine and coastal environments. This review concludes that mangroves are potential candidates to clean up contaminated water, soil, and sediments through their phytoremediation ability. The accumulation of toxic heavy metals by mangroves is mainly through roots with limited upward translocation. Therefore, promoting the maintenance of biodiversity and stability in the coastal environment is recommended as an environmentally friendly and potentially cost-effective approach.

Factors affecting N2O fluxes from heavy metal-contaminated mangrove soils in a subtropical estuary

A 1-year field monitoring program was carried out to observe seasonal variation in N₂O fluxes at two typical mangrove wetlands in a subtropical estuary. The soils in the island-type mangrove wetland had a higher level of heavy metal(loid) contamination and a lower level of salinity compared to the small bay-type mangrove wetland. While there was a high level of similarity in the seasonal variation pattern of N₂O fluxes between the two investigated sites with both being significantly higher in summer than in other seasons, the average of N₂O fluxes in the island-type mangrove wetland was 7.19 μg·m^-2·h^-1， which tended to be lower compared to the small bay-type mangrove wetland (15.63 μg·m^-2·h^-1). Overall, N₂O flux was closely related to soil-borne heavy metal(loid)s, showing a trend to decrease with increasing concentration of these heavy metal(loid)s. The N₂O fluxes increased with decreasing abundance of either denitrifiers or nitrifiers. But the opposite was observed for the anammox bacteria present in the soils. The anammox bacteria were more sensitive to heavy metal(loid) stress but more tolerated high salinity encountered in the investigated soils compared to the denitrifiers or nitrifiers. It appears that anammox reactions mediated by anammox bacteria played a key role in affecting the spatial variation in N₂O fluxes from the mangrove soils in the study area. And an increased level of ammonium in soils tended to promote the activity of anammox bacteria and consequently enhanced N₂O emission from the mangrove soils.

Effects of cadmium and flooding on the formation of iron plaques, the rhizosphere bacterial community structure, and root exudates in Kandelia obovata seedlings

In the rhizosphere, plant root exudates (REs) serve as a bridge between plant and soil functional microorganisms, which play a key role in the redox cycle of iron (Fe). This study examined the effects of periodic flooding and cadmium (Cd) on plant REs, the rhizosphere bacterial community structure, and the formation of root Fe plaques in the typical mangrove plant Kandelia obovata, as well as the relationship between REs and Fe redox cycling bacteria. Based on two-way analysis of variance, flooding and Cd had a considerable effect on the REs of K. obovata. DOC, NH₄⁺-N, NO₃^--N, dissolved inorganic phosphorus, acetic acid, and malonic acid concentrations in REs of K. obovata increased considerably with the increase of Cd concentration under 5 and 10 h flooding conditions. Fe plaque development in the plant root was stimulated by flooding and Cd, although flooding was more effective. After Cd treatment, the ways in which Fe-oxidizing bacteria (FeOB) and Fe-reducing bacteria (FeRB) were enriched in the rhizosphere and rhizoplane of plants were different. Thiobacillus and Sideroxydans (dominant FeOB) were more abundant in the plant rhizosphere, whereas Acinetobacter (dominant FeRB) was more abundant in the rhizoplane. Cd considerably decreased the relative abundance of unclassified_f_Gallionellaceae in the rhizosphere and rhizoplane but dramatically enhanced the relative abundance of Thiobacillus, Shewanella, and unclassified_f_Geobacteraceae. Unclassified_f_Geobacteraceae and Thiobacillus exhibited substantial positive correlations with citric acid and DOC in REs in the rhizosphere and rhizoplane but strong negative correlations with Sideroxydans. The findings indicate that Cd and flooding treatments may play a role in the production and breakdown of Fe plaque in K. obovata roots by affecting the relative abundance of Fe redox cycling bacteria in the rhizosphere and rhizoplane.

Response of bacterial diversity and community structure to metals in mangrove sediments from South China

Human activities have given rise to metal contamination in the constituents of mangrove ecosystems, posing a critical threat to sediment microorganisms; hence, it is of great importance to comprehend the effects of metals on the microbial communities in mangrove sediments. This study was the first to explore the response of the bacterial diversity and community structure to nine metals (As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) in mangrove wetlands from Zhanjiang, China, using 16S rRNA high-throughput sequencing technology and Spearman correlation analysis. The results showed that these nine metals were scattered differently in different mangrove sediments, and the metals and organic matter fractions jointly affected the bacterial communities in the sediments. Several metals displayed significant positive correlations with the abundances of the phylum Bacteroidetes and the genera Actibacter and Sphingobacterium but significant negative correlations with the abundances of two genera Holophaga and Caldithrix. Furthermore, the abundances of the phylum Actinobacteria and many bacterial genera showed significant positive or negative responses to the levels of the three organic matter fractions. Interestingly, the levels of a number of bacterial genera that exhibited increased abundance with high levels of metals and TS might be reduced with high TOC and TN, and vice versa: the levels of genera that exhibited decreased abundance with high levels of metals and TS might be increased with high TOC and TN. Overall, many bacterial groups showed different response patterns to each metal or organic matter fraction, and these metals together with organic matter fractions influenced the bacterial diversity and community structure in mangrove sediments.

Temperature drives the assembly of Bacillus community in mangrove ecosystem

Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO₃-N and NH₄-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.

The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.

The gut microbiome composition of the coral-feeding butterflyfish across Caribbean reefs is more variable at degraded reefs. These microbiomes have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria.

Cultivar-dependent rhizobacteria community and cadmium accumulation in rice: Effects on cadmium availability in soils and iron-plaque formation

The association between the rhizospheric microbial community and Cd accumulation in rice is poorly understood. A field trial was conducted to investigate the different rhizobacterial communities of two rice cultivars with high Cd accumulation (HA) and low Cd accumulation (LA) at four growth stages. Results showed that the Cd content in the roots of the HA cultivar was 1.23 - 27.53 higher than that of the LA cultivar (0.08 - 10.5 µg/plant) at four stages. The LA cultivar had a significantly lower Cd availability in rhizosphere and a higher quantity of iron plaque (IP) on the root surface than the HA cultivar at four stages. This resulted in the reduction of Cd concentration in IPs and Cd translocation from IP-to-root. Microbial analysis indicated that the LA cultivar formed a distinct rhizobacterial community from the HA cultivar and had less α-diversity. The rhizosphere of the LA cultivar was enriched in specific bacterial taxa (e.g., Massilia and Bacillus) involved in Cd immobilization by phosphate precipitation and IP formation by iron oxidization. However, the rhizosphere in the HA cultivar assembled abundant sulfur-oxidizing bacteria (e.g., Sulfuricurvum) and iron reduction bacteria (Geobacter). They promoted Cd mobilization and reduced IP formation via the metal redox process. This study reveals a potential approach in which specific rhizobacteria decrease or increase Cd accumulation in rice on contaminated soil and provides a new perspective for secure rice production.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China

Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO₄^2--S) and Fe but lower concentrations of total phosphorus (TP) and NO₃^--N were detected in ZZW and Qin. Nutrient elements (NO₃^--N, NH₄⁺-N, organic matter (OM), SO₄^2--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO₃^--N was the most important factor. NO₃^--N, SO₄^2--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.

Ecotoxicological assessment of toxic elements contamination in mangrove ecosystem along the Red Sea coast, Egypt

Identifying biochemical aspects of the potentially toxic elements (PTEs) is of particular concern in mangrove ecosystems, Avicennia marina (Forssk.) Vierh., due to their importance as natural buffers in coastal areas. Nonetheless, the microbial community dynamics and potential scavenging responses of mangrove ecosystems to the phytotoxicity of PTEs remain questionable. This study assesses the ecological risk benchmarks of some PTEs, including aluminum (Al), boron (B), barium (Ba), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn), and their microbial responses in the bottom sediments of mangrove ecosystems along Egypt's Red Sea coast. In particular, we assessed the role of microbial metabolites in biochemical cycling of nutrients and scavenging against phytotoxicity hazards. We quantified a spectrum of ecological risk assessment indices, which suggested elevated levels of PTEs in sediment, particularly Cr, Hg, and Pb. Canonical correspondence analysis and generalized linear mixed effects models indicate that the spatial biodiversity of microbial taxa is impacted significantly by the physicochemical characteristics of sediments and concentrations of PTEs. Results demonstrate that the microbial communities and their metabolites exert a significant influence on organic matter (OM) decomposition and the biochemical cycling of phytoavailable nutrients including nitrogen (N), phosphorus (P), and potassium (K). Spatially, nitrogenase activities were higher (411.5 μmoL h^-1 mL^-1) in the southern sites of the Red Sea coast relative to the northern locations (93.8 μmoL h^-1 mL^-1). In contrast, higher concentrations of phytohormones, including indole-3-acetic acid (IAA) (61.5 mg mL^-1) and gibberellins (534.2 mg mL^-1), were more evident in northern sites. Siderophores correlated positively with Fe concentration in sediments and averaged 307.4 mg mL^-1. Overall, these findings provide insights into the biochemical signals of PTEs contamination in hostile environments, contributing to a better understanding of the future prospects of PTEs bioremediation in contaminated coastal environments.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Effects of heavy metals and organic matter fractions on the fungal communities in mangrove sediments from Techeng Isle, South China

Heavy metal pollution has become a serious environmental problem in mangrove ecosystems and has attracted more attention. Most of previous studies have mainly focused on the effects of heavy metals on bacterial communities in mangrove sediments. This study was the first to investigate the effects of heavy metals (e.g., As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) on the fungal communities in mangrove sediments from Techeng Isle, South China. The results of this study indicated that the average contents of Mn, Pb and V of 8.30-161.80 μg/g presented relatively higher pollution levels, while the concentrations of Zn, Cr, Cu and Ni of 0.80-21.93 μg/g were lower than those recorded in other mangrove ecosystems. Furthermore, the sediment fungal community structures responded differently to the nine heavy metals and three organic matter fractions. Heavy metals Cr, Pb and V displayed significant positive correlations with Eutypella (P < 0.05), whereas significant negative correlations with Cystobasidium, Lulworthia, Cladosporium, Lulwoana and Cephalotheca (P < 0.05). In addition, the effects of heavy metals and TS on many fungal genera were opposite to those of TOC and TN. Fungal genera that decreased with high TOC and TN contents may be increased with high heavy metal contents and TS, and vice versa, and the genera that increased with high TOC and TN contents may be decreased with high heavy metals and TS. Our results suggested that many heavy metals, such as Cr, Pb and V, were sensitive to several fungal genera in mangrove sediments, and heavy metals together with organic matter fractions may participate and shape the fungal communities in mangrove sediments.

Sulfate and metal removal from acid mine drainage using sugarcane vinasse as electron donor: Performance and microbial community of the down-flow structured-bed bioreactor

The down flow structured bed bioreactor (DFSBR) was applied to treat synthetic acid mine drainage (AMD) to reduce sulfate, increase the pH and precipitate metals in solutions (Co, Cu, Fe, Mn, Ni and Zn) using vinasse as an electron donor for sulfate-reducing bacteria (SRB). DFSBR achieved sulfate removal efficiencies between 55 and 91%, removal of Co and Ni were obtained with efficiencies greater than 80%, while Fe, Zn, Cu and Mn were removed with average efficiencies of 70, 80, 73 and 60%, respectively. Sulfate reduction increased pH from moderately acidic to 6.7-7.5. Modelling data confirmed the experimental results and metal sulfide precipitation was the mainly responsible for metal removal. The main genera responsible for sulfate and metal reduction were Geobacter and Desulfovibrio while fermenters were Parabacteroides and Sulfurovum. Moreover, in syntrophism with SRB, they played an important role in the efficiency of metal and sulfate removal.

Heavy metal pollution increases CH4 and decreases CO2 emissions due to soil microbial changes in a mangrove wetland: Microcosm experiment and field examination

Mangrove plays an important role in modulating global warming through substantial blue carbon storage relative to their greenhouse gas emission potential. The presence of heavy metals in mangrove wetlands can influence soil microbial communities with implications for decomposition of soil organic matter and emission of greenhouse gases. In this study, field monitoring and a microcosm experiment were conducted to examine the impacts of heavy metal pollution on soil microbial communities and greenhouse gas fluxes. The results show that heavy metal pollution decreased the richness and diversity of the overall soil microbial functional groups (heterotrophs and lithotrophs); however, it did not inhibit the activities of the methanogenic communities, possibly due to their stronger tolerance to heavy metal toxicity compared to the broader soil microbial communities. Consequently, the presence of heavy metals in the mangrove soils significantly increased the emission of CH₄ while the emission of CO₂ as a proxy of soil microbial respiration was decreased. The soil organic carbon content could also buffer the effect of heavy metal pollution and influence CO₂ emissions due to reduced toxicity to microbes. The findings have implications for understanding the complication of greenhouse gas emissions by heavy metal pollution in mangrove wetlands.

Bioavailable metal(loid)s and physicochemical features co-mediating microbial communities at combined metal(loid) pollution sites

Heavy metal contamination poses considerable threats to various ecosystems, yet little is known about the assembly and adaptation of microbial communities at sites with combined heavy metal(loid) pollution. Here, we examined metal(loid) pollutants and bacterial communities in three zones (Zones Ⅰ, Ⅱ, and Ⅲ) of an abandoned sewage reservoir with different usage years. The contamination level of multiple metal(loid)s was higher in Zone Ⅰ than in the other zones, and arsenic (As), zinc (Zn), selenium (Se), copper (Cu), tin (Sn), molybdenum (Mo), antimony (Sb), cadmium (Cd), lead (Pb), thallium (Tl), and nickel (Ni) were the major contaminants (pollution load index > 1). Bioavailable forms of titanium (Ti), chromium (Cr), Sn, and cobalt (Co) played essential roles in shaping the microbial structure, and physicochemical properties, especially organic matter (OM) and pH, also mediated the microbial diversity and composition in the metal(loid) contaminated zones. Metal-microbe interactions and heatmap analysis revealed that the bioavailability of metal(loid)s promoted the niche partitioning of microbial species. Metal-resistant species were abundant in Zone Ⅰ that had the highest metal-contaminated level, whereas metal-sensitive species prevailed in Zone Ⅲ that had the lowest pollution level. The bioavailable metal(loid)s rather than physicochemical and spatial variables explained a larger portion of the variance in the microbial community, and the homogeneous selection was the dominant ecological process driving the assembly of the microbial community. Overall, our study highlighted the importance of metal(loid) bioavailability in shaping microbial structure, future bioremediation, and environmental management of metal(loid) contaminated sites.

Heavy metal pollution and ecological risk assessment in the Maowei sea mangrove, China

The level and ecological impact of heavy metal pollution in the Maowei Sea mangrove are poorly understood. This work first investigated the distribution and ecological risk of Cd, Co, Cr, Cu, Mn, Ni, Pb, and Zn in Maowei Sea mangrove sediments. The results showed that heavy metals were mainly concentrated in the top 10 cm of mangrove stands, declined up to 20 cm deep, and were constant afterwards. Exceptionally, Mn concentration increased significantly with depth in the mudflat. Multiple environmental risk indices indicated that the investigated area was broadly contaminated by heavy metals and that Cd was the dominant contributor to potential ecological risks. However, the biological toxicity posed by these metals was negligible. Multivariate analyses implied that Cd, Co, Cr, Cu, Ni, Pb, and Zn originated mainly from anthropogenic sources, whereas Mn was primarily from natural processes. These findings could provide insightful information for future management of this mangrove.

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes.

Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports

Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effects of organic and inorganic co-contamination on the prokaryotic communities in sediments from three Mediterranean ports. The structure and composition of the bacterial and archaeal communities were assessed by targeted metagenomic analysis of the 16S rRNA gene, and the links of prokaryotic communities with environmental and pollution variables were investigated. The harbors presented pronounced site-specificity in the environmental properties and pollution status. Consistently, the structure of archaeal and bacterial communities in surface sediments exhibited a strong spatial variation among the three investigated ports. On the contrary, a wide overlap in composition of prokaryotic assemblages among sites was found, but local variation in the community composition and loss of prokaryotic diversity was highlighted in a heavily impacted port sector near a shipyard. We provided evidences that organic matter, metals and PAHs as well as temperature and salinity play a strong role in structuring benthic bacterial communities significantly contributing to the understanding of their responses to anthropogenic perturbations in marine coastal areas. Among metals, copper was recognized as strongly associated with the observed changes in bacterial assemblages. Overall, this study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.