Biogeochemical Processes of C and N in the Soil of Mangrove Forest Ecosystems

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.

Remediation of soda-saline-alkali soil through soil amendments: Microbially mediated carbon and nitrogen cycles and remediation mechanisms

Due to the high salt content and pH value, the structure of saline-sodic soil was deteriorated, resulting in decreased soil fertility and inhibited soil element cycling. This, in turn, caused significant negative impacts on crop growth, posing a major challenge to global agriculture and food security. Despite numerous studies aimed at reducing the loss of plant productivity in saline-sodic soils, the knowledge regarding shifts in soil microbial communities and carbon/nitrogen cycling during saline-sodic soil improvement remains incomplete. Consequently, we developed a composite soil amendment to explore its potential to alleviate salt stress and enhance soil quality. Our findings demonstrated that the application of this composite soil amendment effectively enhanced microbial salinity resistance, promotes soil carbon fixation and nitrogen cycling, thereby reducing HCO3- concentration and greenhouse gas emissions while improving physicochemical properties and enzyme activity in the soil. Additionally, the presence of CaSO4 contributed to a decrease in water-soluble Na+ content, resulting in reduced soil ESP and pH by 14.64 % and 7.42, respectively. Our research presents an innovative approach to rehabilitate saline-sodic soil and promote ecological restoration through the perspective of elements cycles.

Dynamics of tannin variations in mangrove leaf litter decomposition and their effects on environmental nitrogen and microbial activity

Tannins play vital roles in regulating ecological processes in mangrove forests. However, how tannins affect nitrogen (N) cycling and microbial metabolism in mangrove ecosystems remains largely unexplored. In this study, we hypothesized the types and amounts of tannins released into seawater and sediments during leaf litter decomposition differed among mangrove plant species, thus their effects on N and microbial metabolism also varied. The alterations of tannins, and environmental N and microbial metabolism during leaf litter decomposition of Kandelia obovata, Avicennia marina, and Sonneratia apetala were evaluated by a microcosm-simulated tidal system. Results showed that total polyphenols (TPs) in seawater treated with K. obovata litter were significantly higher than those in A. marina and S. apetala treatments, although the trends of TP changes elicited an initial increase followed by a decrease during decomposition. The dynamic changes in TPs reduced the seawater N concentrations in K. obovata treatment but not in A. marina and S. apetala treatments. The results of microbial metabolism analysis revealed that leaf litter significantly increased microbial metabolic activities and diversities. The types of carbon sources utilized by sediment microorganisms differed among treatments, with the microbes in S. apetala and A. marina litter used more varieties of amino acids, lipids and sugars than those in K. obovata treatment, probably due to the rich amount of hydrolysable tannins (HTs) in the first two species while the last species only contained ondensed tannins (CTs). CTs released from K. obovata leaf litter not only bound nitrogen-containing macromolecular compounds such as amino acids and proteins but also carbohydrates like polysaccharides, which decreased the supply of C and N to sediment microbiota. These results reveal that the release of mangrove tannins during leaf litter decomposition is one of the key factors driving N cycling, and microbial activities and diversities in mangrove wetlands.

Effects of periodic drying-wetting on microbial dynamics and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in intertidal wetland sediments

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH₄) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH₄, which may help accurately project CH₄ emission from intertidal wetlands under different tidal scenarios.

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.

Microbial community development in tropical constructed wetland soils in Taiwan

Constructed wetlands are widely used around the world as a low-cost wastewater treatment system that simultaneously provides various ecosystem services. Microorganisms in wetland soils serve as fundamental producers and decomposers that support wetland functions. However, few studies have documented the compositions of soil microorganisms in constructed wetland systems and even fewer have evaluated how soil microorganisms change after a wetland is constructed. In this study, soil samples were collected from four constructed wetlands of different ages and analyzed with a phospholipid fatty acid (PLFA) method to show how soil microbial communities change overtime. The results were that both the bacterial and fungal abundances increased with wetland age, and bacteria comprised about 90% of the soil microbial communities in all ages of constructed wetlands. Although the compositions of microbial communities remained similar among the wetlands, the stress indices showed that microbial stress may be affected by changes in the availability of in situ nutrients, e.g. ammonium, nitrate_, soluble organic nitrogen and total dissolved nitrogen.

Differential Response of Macrobenthic Abundance and Community Composition to Mangrove Vegetation

The mass planting of mangroves has been proposed as a mitigation strategy to compensate for mangrove loss. However, the effects of mangrove vegetation on the abundance and community composition of macrobenthos remain controversial. The macrobenthic communities in four intact mangrove forests with different conditions and the adjacent nonvegetated mudflats of two mangrove species with distinct stand structures on the western coast of Taiwan were examined. Some macrobenthic taxa occurred only in the mangroves, suggesting macrobenthic critical habitats. Seasonal shift in community composition was more pronounced in the mudflats than in the mangroves, possibly due to the rich food supply, low temperature, and shelter function provided by mangrove forests. However, crab density was always lower in the mangroves than in the mudflats. There was a negative relationship between the stem density of Kandelia obovata (S., L.) and infaunal density. The pneumatophore density of Avicennia marina (Forsk.) correlated negatively with epifaunal density. Our results show that the response of macrobenthic abundance and community composition to mangrove vegetation was inconsistent. We reason that mangroves are critical habitats for the macrobenthos in the mudflats. However, if mangrove tree density is high, we predict that the macrobenthic density will decrease. This suggests that at some intermediate level of mangrove tree density, where there are enough mangrove trees to harbor a macrobenthic community but not enough trees to significantly reduce this density, mangroves management can be optimally achieved to promote the presence of a diverse and dense macrobenthic community.

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.

Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent

Mangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem health. In this study, we used 16S rRNA gene analysis, metabolic inference, nutrient concentrations, and δ¹³C and δ¹⁵N isotopes to evaluate the impact of land use change on near-shore biogeochemical cycles and microbial community structures within mangrove-dominated estuaries. Samples in close proximity to active shrimp aquaculture were high in NH₄⁺, NO₃⁻ NO₂⁻, and PO₄³⁻; lower in microbial community and metabolic diversity; and dominated by putative nitrifiers, denitrifies, and sulfur-oxidizing bacteria. Near intact mangrove forests we observed the presence of potential nitrogen fixers of the genus Calothrix and order Rhizobiales. We identified possible indicators of aquaculture effluents such as Pseudomonas balearica, Ponitmonas salivibrio, family Chromatiaceae, and genus Arcobacter. These results highlight the sensitivity of the estuarine-mangrove microbial community, and their ecosystem functions, to land use changes.

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In near-intact mangrove forests, we observed the presence of nitrogen fixers

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Calothrix could play a role in increasing nitrogen inventories via nitrogen fixation

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Disturbed sites were correlated with increased nitrogen and reduction in diversity

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Disturbed sites were dominated by nitrifiers, denitrifies, and sulfur-oxidizing bacteria

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation.

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.

Niche Differentiation of Active Methane-Oxidizing Bacteria in Estuarine Mangrove Forest Soils in Taiwan

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10-15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils.