Microbial diversity in Brazilian mangrove sediments - a mini review

The diversity, drivers, consequences and management of plant invasions in the mangrove ecosystems

Mangrove ecosystems, which occupy intertidal environments across tropical and subtropical regions, provide crucial ecosystem services, such as protecting the coastal areas by reducing the impact of cyclones, storms, and tidal waves. Anthropogenic activities such as human settlements, deforestation, pollution, and climate change have increased the risk of biological invasions in mangrove habitats. Plant species can be introduced to mangrove habitats via anthropogenic means, such as trade and transportation, urbanisation, and agriculture, as well as through natural processes like wind, floods, cyclones, and animal-assisted seed dispersal. Additionally, some native plants can become invasive due to the changes in the mangrove ecosystem. Invasive species can significantly affect coastal ecosystems by out-competing native flora for resources, thereby altering fundamental properties, functions, and ecosystem services of the mangrove forests. The successful establishment of invasive species depends on a complex interplay of factors involving the biological attributes of the invading species and the ecological dynamics of the invaded habitat. This review focuses on exploring the mechanisms of invasion, strategies used by invasive plants, the effects of invasive plants on mangrove habitats and their possible management strategies. Based on the literature, managing invasive species is possible by biological, chemical, or physical methods. Some non-native mangrove species introduced through restoration activities can often become more intrusive than native species. Therefore, restoration activities should prioritise avoiding the use of non-native plant species.

Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions

The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.

Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment

BACKGROUND

Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants.

MATERIALS AND METHODS

The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes.

RESULTS

Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments.

CONCLUSION

This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.

Diversity and assembly patterns of mangrove rhizosphere mycobiome along the Coast of Gazi Bay and Mida Creek in Kenya

Fungi are among key actors in the biogeochemical processes occurring in mangrove ecosystems. In this study, we investigated the changes of fungal communities in selected mangrove species by exploring differences in diversity, structure and the degree of ecological rearrangement occurring within the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) at Gazi Bay and Mida Creek in Kenya. Alpha diversity investigation revealed that there were no significant differences in species diversity between the same mangrove species in the different sites. Rather, significant differences were observed in fungal richness for some of the mangrove species. Chemical parameters of the mangrove sediment significantly correlated with fungal alpha diversity and inversely with richness. The fungal community structure was significantly differentiated by mangrove species, geographical location and chemical parameters. Taxonomic analysis revealed that 96% of the amplicon sequence variants belonged to the Phylum Ascomycota, followed by Basidiomycota (3%). Predictive FUNGuild and co-occurrence network analysis revealed that the fungal communities in Gazi Bay were metabolically more diverse compared to those of Mida Creek. Overall, our results demonstrate that anthropogenic activities influenced fungal richness, community assembly and their potential ecological functions in the mangrove ecosystems investigated.

Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB

Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB ( https://smdb.gxu.edu.cn/ )-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Diversity and Vertical Distribution of Sedimentary Bacterial Communities and Its Association with Metal Bioavailability in Three Distinct Mangrove Reserves of South China

The structure of sedimentary bacterial communities in mangroves depends on environmental factors such as pH, salinity, organic matter content, and metal pollution. To investigate the effect of heavy metal pollution on such communities, core samples of sediments from four sites in three distinct mangrove reserves (Golden Bay Mangrove Reserve in Beihai, Guangxi province (GXJHW), Shankou Mangrove Reserve in Hepu, Guangxi province (GXSK), and MaiPo mangrove in Hong Kong (MPCT and MPFQ)) in South China were analyzed for physicochemical properties, multiple chemical forms of metals, and vertical bacterial diversity. Sedimentary bacterial communities varied greatly among the different sampling sites, with biodiversity decreasing in the order of GXSK, GXJHW, MPFQ, and MPCT. Proteobacteria was the dominant phylum, followed by Chloroflexi, across all four sampling sites. Multivariate statistical analysis of the effect of environmental factors on the sedimentary bacterial communities found that total carbon was the only physicochemical factor with a significant influence at all four sites. The correlations between environmental factors and bacterial structure were weak for the two sites in Guangxi province, but strong at MPCT in Hong Kong where environmental factors were almost all significantly negatively correlated with bacterial diversity. Variance partitioning analysis revealed that physicochemical properties and chemical forms of metals could explain most of the changes in bacterial diversity. Overall, we observed that heavy metal forms were more important than total metal content in influencing the sedimentary bacterial diversity in mangroves, consistent with the more bioavailable metal species having the greatest effect.

Biotechnological applications of mangrove plants and their isolated compounds in medicine-a mechanistic overview

Mangrove plants, also known as halophytes, are ecologically important plants that grow in various tropical and subtropical intertidal regions. Owing to the extreme abiotic and biotic stressful conditions they thrive in, these plants produce unique compounds with promising pharmacological propensities. Mangroves are inhabited by an astronomical number of fungal communities which produce a diverse array of extracellular degradative enzymes, namely: amylase, cellulase, xylanase, pectinase, cholesterol oxidase, etc. Such enzymes can be isolated from the mangrove fungi and harnessed for different biotechnological applications, for example, as replacements for chemical catalysts. Mangrove microbes attract considerable attention as they shelter the largest group of marine microorganisms that are resistant to extreme conditions and can produce novel biogenic substances. Vaccines developed from mangrove microbes may promise a safe future by developing effective immunization procedures with a minimum of economic burden. Interestingly, mangroves offer an exciting opportunity for synthesizing nanoparticles in a greener way as these plants are naturally rich in phytochemicals. Rhizophora mucronata Lam., Avicennia officinalis L. and Excoecaria agallocha L. are capable of synthesizing nanoparticles which have evolved recently as an alternative in various industries and are used for their biomedical application. Besides, the phytoconstituents isolated from mangrove plants, such as: gallic acid, galactose, lupeol, catechins, carotenoids, etc., were explored for various biological activities. These compounds are used in the pharmaceutical and nutraceutical industries to produce antimicrobial, antioxidant, anticancer, antidiabetic, and other therapeutic agents. The present review provides information on the biotechnological potentials of mangrove plants and their bioactive compounds as a new source of novel drugs, enzymes, nanoparticles and therapeutically important microbial pigments. Thus, this review forms a base of support and hasten the urgent research on biomedical applications of mangroves.

A unique bacterial and archaeal diversity make mangrove a green production system compared to rice in wetland ecology: A metagenomic approach

Mangrove provides significant ecosystem services, however, 40% of tropical mangrove was lost in last century due to climate change induced sea-level rise and anthropogenic activities. Sundarban-India, the largest contiguous mangrove of the world lost 10.5% of its green during 1930-2013 which primarily converted to rice-based systems. Presently degraded mangrove and adjacent rice ecology in Sundarban-India placed side by side and create typical ecology which is distinct in nature in respect to soil physicochemical properties, carbon dynamics, and microbial diversities. We investigated the structural and functional diversities of bacteria and archaea through Illumina MiSeq metagenomic analysis using V3-V4 region of 16S rRNA gene approach that drives greenhouse gases emission and carbon-pools. Remote sensing-data base were used to select the sites for collecting the soil and gas samples. The methane and nitrous oxide emissions were lower in mangrove (-0.04 mg m^-2 h^-1 and -52.8 μg m^-2 h^-1) than rice (0.26 mg m^-2 h^-1 and 44.7 μg m^-2 h^-1) due to less availability of carbon-substrates and higher sulphate availability (85.8% more than rice). The soil labile carbon-pools were more in mangrove, but lower microbial activities were noticed due to stress conditions. A unique microbial feature indicated by higher methanotrophs: methanogens (11.2), sulphur reducing bacteria (SRB): methanogens (93.2) ratios and lower functional diversity (7.5%) in mangrove than rice. These could be the key drivers of lower global warming potential (GWP) in mangrove that make it a green production system. Therefore, labile carbon build-up potential (38%) with less GWP (63%) even in degraded-mangrove makes it a clean production system than wetland-rice that has high potential to climate change mitigation. The whole genome metagenomic analysis would be the future research priority to identify the predominant enzymatic pathways which govern the methanogenesis and methanotrophy in this system.

Isolation and enzyme bioprospection of bacteria associated to Bruguiera cylindrica, a mangrove plant of North Sumatra, Indonesia

Mangrove-associated bacteria are of industrial interest due to their diverse and versatile enzyme properties. This study investigates the culturable bacteria from a wide range of habitat in a Bruguiera cylindrica mangrove ecosystem in North Sumatra. Screening of extracellular hydrolytic enzymes showed multiple potential traits in amylase, cellulase, chitinase, phosphatase, protease, and urease production by bacterial isolates. Molecular identification based on 16S rDNA region of a potential strain, Vibrio alginolyticus Jme3-20 is then reported as a newly proteolytic agent. The strain also showed a stable growth under salinity (NaCl) stress with considerable phosphate solubilization activities. Protease activity was enhanced by optimizing the 0.5 % (w/v) sucrose and soy peptone in the fermentation medium. SDS-PAGE and zymogram analysis showed the presence of a 35-kDa MW protease. Hence, our study revealed important insights into the bacterial diversity and activity in mangrove ecosystems, evidencing the importance of microbial exploration in this ecosystem.

Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales

We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).

Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.

Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially the variations between pristine and anthropogenic mangroves. To elucidate this, we investigated the microbial taxonomic and functional shifts of the mangrove microbiomes and their potential for bioactive compounds in two different coastal mangrove ecosystems in southern China. A gene catalogue, including 87 million unique genes, was constructed, based on deep shotgun metagenomic sequencing. Differentially enriched bacterial and archaeal taxa between pristine mangroves (Guangxi) and anthropogenic mangroves (Shenzhen) were found. The Nitrospira and ammonia-oxidizing archaea, specifically, were more abundant in Shenzhen mangroves, while sulfate-reducing bacteria and methanogens were more abundant in Guangxi mangroves. The results of functional analysis were consistent with the taxonomic results, indicating that the Shenzhen mangrove microbiome has a higher abundance of genes involved in nitrogen metabolism while the Guangxi mangrove microbiome has a higher capacity for sulfur metabolism and methanogenesis. Biosynthetic gene clusters were identified in the metagenome data and in hundreds of de novo reconstructed nonredundant microbial genomes, respectively. Notably, we found different biosynthetic potential in different taxa, and we identified three high quality and novel Acidobacteria genomes with a large number of BGCs. In total, 67,278 unique genes were annotated with antibiotic resistance, indicating the prevalence and persistence in multidrug-resistant genes in the mangrove microbiome.

IMPORTANCE This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.

Variations of soil bacterial diversity and metabolic function with tidal flat elevation gradient in an artificial mangrove wetland

Understanding the sensitivity of soil bacteria to environmental fluctuations can enhance the management of microbial ecosystem services in artificial mangrove wetlands. In this study, the variation in bacterial diversity and metabolic functions in different compartments (bulk soil, rhizosphere soil, and rhizoplane) of the soil and mangrove plant along the tidal elevation gradient was studied in Xiatanwei (Xiamen China) mangrove wetland park, a Kandelia obovata-dominated artificial mangrove stand. With the increase of the tidal flat elevation, the soil pH, total organic matter, and soil moisture contents decreased significantly, while the soil electric conductivity and redox potential increased significantly. The bacterial diversity in the bulk soil and the rhizosphere soil both decreased with the elevation of tidal levels. The relative abundance of the dominant phyla in the bulk and rhizosphere soils decreased with the rise of the tidal flat level. A significant rhizosphere effect was observed in the roots of K. obovata that the rhizosphere soil had higher bacterial diversity and richness than that in the bulk soil nearby. The rhizosphere soil of K. obovata at the low-tidal flat was enriched with the genera Nitrospira and Planctomycetes, which are valuable for the mangrove ecosystem. The Chao1 estimator and Shannon index of the bacterial community in the rhizoplane of K. obovata were much lower than that in the rhizosphere and bulk soils. Results of Biolog-Eco assay show that the bacterial groups in low tidal flat bulk soil had the highest ability in utilizing the carbon sources, which was indicated by the high values of average well color development and the high McIntosh index, and the utilization ability of carbon source decreased with the increase of tidal flat levels. The variation of the soil humidity and Eh jointly shaped the diversity and metabolic function of soil bacterial communities along the tidal flat elevation gradient.

Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil

While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.

Potential bacterial bioindicators of urban pollution in mangroves

Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

Tracking Mangrove Oil Bioremediation Approaches and Bacterial Diversity at Different Depths in an in situ Mesocosms System

In this study, oil spills were simulated in field-based mangrove mesocosms to compare the efficiency of bioremediation strategies and to characterize the presence of the alkB, ndo, assA, and bssA genes and the ecological structures of microbial communities in mangrove sediments at two different depths, (D1) 1–10 cm and (D2) 25–35 cm. The results indicated that the hydrocarbon degradation efficiency was higher in superficial sediment layers, although no differences in the hydrocarbon degradation rates or in the abundances of the alkB and ndo genes were detected among the tested bioremediation strategies at this depth. Samples from the deeper layer exhibited higher abundances of the analyzed genes, except for assA and bssA, which were not detected in our samples. For all of the treatments and depths, the most abundant phyla were Proteobacteria, Firmicutes and Bacteroidetes, with Gammaproteobacteria, Flavobacteriales and Clostridiales being the most common classes. The indicator species analysis (ISA) results showed strong distinctions among microbial taxa in response to different treatments and in the two collection depths. Our results indicated a high efficiency of the monitored natural attenuation (MNA) for oil consumption in the tested mangrove sediments, revealing the potential of this strategy for environmental decontamination and suggesting that environmental and ecological factors may select for specific bacterial populations in distinct niches.

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.

IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains

BACKGROUND

Studies carried out with novel 13 strains of Trichoderma, isolated from mangrove sediments (PE, Brazil) using morphophysiological and molecular characterization, followed evaluation of biocontrol using Fusarium strains isolated from Caatinga soil (PE, Brazil). Trichoderma strains were characterized by polyphasic taxonomic approach, and the extracted DNA was amplified with primers ITS 1 and 4, and sequenced. The biocontrol evaluation was conducted at 24 and 48 h of growth intervals by Tukey test, with a significance of 5%. Antibiosis tests were assessed in vitro by dual plate and partition plate techniques against Fusarium strains.

RESULTS

Trichoderma molecular identification, sequences of 500 bp were amplified, deposited into GenBank, and used for phylogenetic analyses. The strains were identified as T. asperellum (10), as T. harzianum (2) and one as T. longibrachiatum. Growth rate presented an average of 0.1207 cm h-1 for Trichoderma and lower growth rate of 0.031 cm h-1 for Fusarium spp., respectively. Antibiosis tests presented the best antagonist level of efficiency for T. asperellum UCP 0149 against F. solani UCP 1395 (82.2%) and F. solani UCP 1075 (70.0%), followed by T. asperellum UCP 0319 against F. solani UCP1083 (73.4%) and T. asperellum UCP 0168 against F. solani UCP1098 (71.5%), respectively.

CONCLUSIONS

The data obtained in this study as tool for identification of novel Trichoderma strains serve as basis for development of several sustainable use for biotechnological processes. Those Trichoderma strains found promising for the management antagonistic potential and interaction could aid the conduct of biotechnological biocontrol of contaminants, and improve environmental conditions for the health of plants.

Three New Isoflavonoid Glycosides from the Mangrove-Derived Actinomycete Micromonospora aurantiaca 110B

The mangrove ecosystem is a rich resource for the discovery of actinomycetes with potential applications in pharmaceutical science. Besides the genus Streptomyces, Micromonospora is also a source of new bioactive agents. We screened Micromonospora from the rhizosphere soil of mangrove plants in Fujian province, China, and 51 strains were obtained. Among them, the extracts of 12 isolates inhibited the growth of human lung carcinoma A549 cells. Strain 110B exhibited better cytotoxic activity, and its bioactive constituents were investigated. Consequently, three new isoflavonoid glycosides, daidzein-4'-(2-deoxy-α-l-fucopyranoside) (1), daidzein-7-(2-deoxy-α-l-fucopyranoside) (2), and daidzein-4',7-di-(2-deoxy-α-l-fucopyranoside) (3) were isolated from the fermentation broth of strain 110B. The structures of the new compounds were determined by spectroscopic methods, including 1D and 2D nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry (HR-ESIMS). The result of medium-changing experiments implicated that these new compounds were microbial biotransformation products of strain M. aurantiaca 110B. The three compounds displayed moderate cytotoxic activity to the human lung carcinoma cell line A549, hepatocellular liver carcinoma cell line HepG2, and the human colon tumor cell line HCT116, whereas none of them showed antifungal or antibacterial activities.

Fungal communities in oil contaminated mangrove sediments - Who is in the mud?

Mangroves are ecosystems located in tropical and subtropical regions of the world and are vital for coastal protection. Their unique characteristics make them hotspots for carbon cycling and biological diversity. Studies on isolated filamentous fungi and environmental and anthropogenic factors that influence sediments offer new understandings on how to preserve mangroves. Here we report on the filamentous fungi isolated from four mangroves. We correlated fungal community composition with sediment texture, polycyclic aromatic hydrocarbons concentration (oil pollution), pH, salinity, organic matter, total and thermotolerant coliforms (sewage pollution). In total we identified 34 genera and 97 species. The most polluted sites had highest species richness whereas the best preserved site showed the lowest species richness. Oil spill and sewage pollution were identified as the drivers of fungal community composition in the most polluted sites. We found very distinct fungal communities with no >5 species shared between any two mangrove sites.

Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest

Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.

Influence of ancient anthropogenic activities on the mangrove soil microbiome

Mangroves are highly productive ecosystems located at the transition between the terrestrial and marine environments. Mangroves play an important role in carbon storage, nutrient cycling and support for the marine food web. Mangrove soils are formed by fine particles rich in organic carbon and are subject to constant fluctuations in oxygen, salinity and nutrient availability due to fresh water flux and tidal variations. Microbes play an important role in nutrient cycling in mangrove soils; however, studies on the mangrove soil microbiome are scarce. Here we compare the microbiome of pristine mangrove soil located in an environmentally protected area in Guaratuba, Southern Brazil, with the microbiome of mangrove soil affected by the presence of carbonaceaous debris eroding from an archeological site known as Sambaqui. We show that although the Sambaqui site has a major effect on soil chemistry, increasing the soil pH by 2.6 units, only minor changes in the soil microbiome were detected indicating resilience of the microbial community to pH variations. The high alpha diversity indexes and predicted metabolic potential suggest that the mangrove soil microbiome not only provides important ecological services but also may host a broad range of microbes and genes of biotechnological interest.

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems

The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.

Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana

Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.

Novel Salt-Tolerant Xylanase from a Mangrove-Isolated Fungus Phoma sp. MF13 and Its Application in Chinese Steamed Bread

A novel glycosyl hydrolase family 11 xylanase gene, xynMF13A, was cloned from Phoma sp. MF13, a xylanase-producing fungus isolated from mangrove sediment. xynMF13A was heterologously expressed in Pichia pastoris, and the recombinant XynMF13A (rXynMF13A) was purified by Ni-affinity chromatography. The temperature and pH optima of purified rXynMF13A were 45 °C and pH 5.0, respectively. rXynMF13A showed a high level of salt tolerance, with maximal enzyme activity being seen at 0.5 M NaCl and as much as 53% of maximal activity at 4 M NaCl. The major rXynMF13A hydrolysis products from corncob xylan were xylobiose, xylotriose, xylotetraose, and xylopentaose, but no xylose was found. These hydrolysis products suggest an important potential for XynMF13A in the production of xylooligosaccharides (XOs). Furthermore, rXynMF13A had beneficial effects on Chinese steamed bread production, by increasing specific volume and elasticity while decreasing hardness and chewiness. These results demonstrate XynMF13A to be a novel xylanase with potentially significant applications in baking, XOs production, and seafood processing.

Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem

In mangrove environments, bacterioplankton communities constitute an important component of aquatic biota and play a major role in ecosystem processes. Variability of bacterioplankton communities from Sundarbans mangrove, located in the Indian subcontinent in South Asia and sits on the apex of Bay of Bengal, was investigated over monsoon and post-monsoon seasons. The study was undertaken in two stations in Sundarbans using 16S rRNA clone library and Illumina MiSeq approaches with focus on the functionally important members that participate in coastal biogeochemical cycling. Out of 544 sequenced clones, Proteobacteria dominated the study area (373 sequences) with persistence of two major classes, namely, Gammaproteobacteria and Alphaproteobacteria across both monsoon and post-monsoon seasons in both stations. Several sequences belonging to Sphingomonadales, Chromatiales, Alteromonadales, Oceanospirillales, and Bacteroidetes were encountered that are known to play important roles in coastal carbon cycling. Some sequences showed identity with published uncultured Planctomycetes and Chloroflexi highlighting their role in nitrogen cycling. The detection of two novel clades highlighted the existence of indigenous group of bacterioplankton that may play important roles in this ecosystem. The eubacterial V3-V4 region from environmental DNA extracted from the above two stations, followed by sequencing in Illumina MiSeq system, was also targeted in the study. A congruency between the clone library and Illumina approaches was observed. Strong variability in bacterioplankton community structure was encountered at a seasonal scale in link with precipitation. Drastic increase in sediment associated bacteria such as members of Firmicutes and Desulfovibrio was found in monsoon hinting possible resuspension of sediment-dwelling bacteria into the overlying water column. Principal component analysis (PCA) revealed dissolved ammonium and dissolved nitrate to account for maximum variation observed in the bacterioplankton community structure. Overall, the study showed that a strong interplay exists between environmental parameters and observed variability in bacterioplankton communities as a result of precipitation which can ultimately influence processes and rates linked to coastal biogeochemical cycles.

Screening of Bacillus strains isolated from mangrove ecosystems in Peninsular Malaysia for microplastic degradation

The continuous accumulation of microplastics in the environment poses ecological threats and has been an increasing problem worldwide. In this study, eight bacterial strains were isolated from mangrove sediment in Peninsular Malaysia to mitigate the environmental impact of microplastics and develop a clean-up option. The bacterial isolates were screened for their potential to degrade UV-treated microplastics from polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), and polystyrene (PS). Only two isolates, namely, Bacillus cereus and Bacillus gottheilii, grew on a synthetic medium containing different microplastic polymers as the sole carbon source. A shake flask experiment was carried out to further evaluate the biodegradability potential of the isolates. Degradation was monitored by recording the weight loss of microplastics and the growth pattern of the isolates in the mineral medium. The biodegradation extent was validated by assessment of the morphological and structural changes through scanning electron microscopy and Fourier transform infrared spectroscopy analyses. The calculated weight loss percentages of the microplastic particles by B. cereus after 40 days were 1.6%, 6.6%, and 7.4% for PE, PET, and PS, respectively. B. gottheilii recorded weight loss percentages of 6.2%, 3.0%, 3.6%, and 5.8% for PE, PET, PP, and PS, respectively. The designated isolates degraded the microplastic material and exhibited potential for remediation of microplastic-contaminated environment. Biodegradation tests must be conducted to characterize the varied responses of microbes toward pollutants, such as microplastics. Hence, a novel approach for biodegradation of microplastics must be developed to help mitigate the environmental impact of plastics and microplastic polymers.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Bacterial interactions and implications for oil biodegradation process in mangrove sediments

Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach

Covering a quarter of the world's tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%-85%), while Basidiomycota was less abundant (14%-24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.

Physiological aspects of mangrove (Laguncularia racemosa) grown in microcosms with oil-degrading bacteria and oil contaminated sediment

To assess the severity of oil spills on mangroves, diagnosis of the vegetation health is crucial. Some aspects of photosynthesis such as photochemical efficiency and leaf pigment composition together with the level of oxidative stress may constitute reliable indicators for vegetation health. To test this approach 14 month old Laguncularia racemosa were contaminated with 5 L m(-2) of the marine fuel oil MF-380 and treated with an oil degrading bacterial consortium in microcosms. Contamination resulted in a 20% decrease in shoot dry weight after 128 days. Photochemical efficiency, pigment content, catalase and ascorbate peroxidase remained unchanged. Multivariate ordination of DGGE microbial community fingerprints revealed a pronounced separation between the oil contaminated and the non-contaminated samples. Further studies are necessary before physiological parameters can be recommended as indicators for plant's health in oil polluted mangroves.