Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes

Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].

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.

Estuarine mangrove niches select cultivable heterotrophic diazotrophs with diverse metabolic potentials-a prospective cross-dialog for functional diazotrophy

Introduction

Biological nitrogen fixation (BNF), an unparalleled metabolic novelty among living microorganisms on earth, globally contributes ~88-101 Tg N year-1 to natural ecosystems, ~56% sourced from symbiotic BNF while ~22-45% derived from free-living nitrogen fixers (FLNF). The success of symbiotic BNF is largely dependent on its interaction with host-plant, however ubiquitous environmental heterotrophic FLNFs face many limitations in their immediate ecological niches to sustain unhindered BNF. The autotrophic FLNFs like cyanobacteria and oceanic heterotrophic diazotrophs have been well studied about their contrivances acclimated/adapted by these organisms to outwit the environmental constraints for functional diazotrophy. However, FLNF heterotrophs face more adversity in executing BNF under stressful estuarine/marine/aquatic habitats.

Methods

In this study a large-scale cultivation-dependent investigation was accomplished with 190 NCBI accessioned and 45 non-accessioned heterotrophic FLNF cultivable bacterial isolates (total 235) from halophilic estuarine intertidal mangrove niches of Indian Sundarbans, a Ramsar site and UNESCO proclaimed World Heritage Site. Assuming ~1% culturability of the microbial community, the respective niches were also studied for representing actual bacterial diversity via cultivation-independent next-generation sequencing of V3-V4 rRNA regions.

Results

Both the studies revealed a higher abundance of culturable Gammaproteobacteria followed by Firmicutes, the majority of 235 FLNFs studied belonging to these two classes. The FLNFs displayed comparable selection potential in media for free nitrogen fixers and iron-oxidizing bacteria, linking diazotrophy with iron oxidation, siderophore production, phosphorus solubilization, phosphorus uptake and accumulation as well as denitrification.

Discussion

This observation validated the hypothesis that under extreme estuarine mangrove niches, diazotrophs are naturally selected as a specialized multidimensional entity, to expedite BNF and survive. Earlier metagenome data from mangrove niches demonstrated a microbial metabolic coupling among C, N, P, S, and Fe cycling in mangrove sediments, as an adaptive trait, evident with the co-abundant respective functional genes, which corroborates our findings in cultivation mode for multiple interrelated metabolic potential facilitating BNF in a challenging intertidal mangrove environment.

Storage and dynamics of soil organic carbon in allochthonous-dominated and nitrogen-limited natural and planted mangrove forests in southern Thailand

Mangrove forests can help to mitigate climate change by storing a significant amount of carbon (C) in soils. Planted mangrove forests have been established to combat anthropogenic threats posed by climate change. However, the efficiency of planted forests in terms of soil organic carbon (SOC) storage and dynamics relative to that of natural forests is unclear. We assessed SOC and nutrient storage, SOC sources and drivers in a natural and a planted forest in southern Thailand. Although the planted forest stored more C and nutrients than the natural forest, the early-stage planted forest was not a strong sink relative to mudflat. Both forests were predominated by allochthonous organic C and nitrogen limited, with total nitrogen being a major driver of SOC in both cases. SOC showed a significant decline along land-to-sea and depth gradients as a result of soil texture, nutrient availability, and pH in the natural forest.

The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests

Coastal wetlands such as mangrove forests are breeding grounds for nuisance-causing insects. Rotational Impoundment Management (RIM) for mosquito control involves annual summer inundation of impounded mangrove forests with estuarine water during the summer half year. However, in addition to controlling mosquitos, RIM may change biogeochemical pathways. This study set out to investigate how RIM quantitatively affects physicochemical soil characteristics and potential nitrifying and denitrifying activities (PNA and PDA), which are key in the global nitrogen cycle. Before and after the implementation of RIM, soil samples were collected annually in habitats differing in size and abundance of black mangroves (Avicennia germinans) in an impoundment with RIM and in an adjacent impoundment with a more open connection to the lagoon. Compared to the non-managed impoundment, soil moisture content, total nitrogen and PDA increased, while salinity decreased after the start of annual summer flooding, but only in the dwarf habitat. In the sparse and dense habitats, total nitrogen and PDA increased independently of summer flooding, whereas soil moisture content and salinity were not affected by RIM. Labile organic nitrogen increased only in the RIM impoundment, irrespective of the habitat type. PNA was generally not affected with time, except in the dwarf habitat in the absence of intentional summer flooding where it increased. Changes in the non-managed impoundment adjacent to the RIM impoundment demonstrate the importance of groundwater exchange in linked ecosystems. The consequences of interventions in the management of mangrove impoundments and adjacent forests for the nitrogen budget are discussed.

Riverine and submarine groundwater nutrients fuel high primary production in a tropical bay

River discharge has long been recognized as a major source of nutrients supporting high primary production (PP) in Bandon Bay, while submarine groundwater discharge (SGD) and atmospheric deposition have largely been overlooked. In this study, we evaluated contributions of nutrients via river, SGD and atmospheric deposition, and their roles on PP in the bay. Contribution of nutrients from the three sources during different time of the year was estimated. Nutrients supply from Tapi-Phumduang River accounted for two-fold the amount from SGD while very little supply was from atmospheric deposition. Significant seasonal difference in silicate and dissolved inorganic nitrogen were observed in river water. Dissolved phosphorous in river water was mainly (80 % to 90 %) of DOP in both seasons. For the bay water, DIP in wet season was two-fold higher than in dry season while dissolved organic phosphorus (DOP) was only one half of those measured in dry season. In SGD, dissolved nitrogen was mostly inorganic (with 99 % as NH₄⁺), while dissolved phosphorous was predominantly (DOP). In general, Tapi River is the most important source of nitrogen (NO₃^-, NO₂^-, and DON), contributing >70 % of all considered sources, especially in wet season, while SGD is a major source for DSi, NH₄⁺ and phosphorus, contributing 50 % to 90 % of all considered sources. To this end, Tapi River and SGD deliver a large quantity of nutrients and support high PP in the bay (337 to 553 mg-C m^-2 day^-1).

Interspecific variations in leaf litter decomposition and nutrient release from tropical mangroves

Efficient nutrient cycling through decomposition of leaf litter often regulates the high productivity and subsequent carbon sequestration of mangrove ecosystems along the land-ocean boundary. To understand the characteristics and the potentials of mangrove leaf litter in supplying organic carbon and nutrients to the coastal waters, four major mangrove species (A. officinalis, R. mucronata, H. littoralis and S. apetala) of Bhitarkanika mangrove forest, Odisha, India, were examined in controlled environmental conditions. Half-life time (t₀.₅), estimated for decomposition of those mangrove leaf litter materials ranged from 18 to 52 days. During the incubation experiment, organic carbon from mangrove leaf litter was released primarily through physical processes and was available for heterotrophic respiration. Among the four species, leaf litter of S. apetala with the lowest initial C/N ratios, released organic carbon with low molecular weight (labile substances) that has a relatively higher potential to support the aquatic food web. On the contrary, leaf litter of R. mucronata released organic material with relatively higher molecular weight (humic substances, higher aromaticity), which revealed its superior non-labile characteristics in this unique environment. The mean total heterotrophic bacterial (THB) population in the incubation was around nine-fold higher than the control. THB population growth and Chromophoric Dissolved Organic Matter (CDOM) spectral data further suggested the rapid release of highly labile and recalcitrant carbon from S. apetala and R. mucronata (between 7th and 21st day of incubation), respectively. The mean litter fall from the Bhitarkanika mangrove forest was estimated to be 11.32 ± 1.57 Mg ha^-1 y^-1 and its corresponding carbon content was 5.43 ± 0.75 Mg C ha^-1. The study revealed the role of leaf litter leachates as an important food source to microbial communities in the adjacent coastal waters, in addition to a potential carbon sequesterer through long-term burial in mangrove soil and export to the deep sea.

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.

Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations

Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.

Fate of Dissolved Nitrogen in a Horizontal Levee: Seasonal Fluctuations in Nitrate Removal Processes

Horizontal levees are a nature-based approach for removing nitrogen from municipal wastewater effluent while simultaneously providing additional benefits, such as flood control. To assess nitrogen removal mechanisms and the efficacy of a horizontal levee, we monitored an experimental system receiving nitrified municipal wastewater effluent for 2 years. Based on mass balances and microbial gene abundance data, we determined that much of the applied nitrogen was most likely removed by heterotrophic denitrifiers that consumed labile organic carbon from decaying plants and added wood chips. Fe(III) and sulfate reduction driven by decay of labile organic carbon also produced Fe(II) sulfide minerals. During winter months, when heterotrophic activity was lower, strong correlations between sulfate release and nitrogen removal suggested that autotrophic denitrifiers oxidized Fe(II) sulfides using nitrate as an electron acceptor. These trends were seasonal, with Fe(II) sulfide minerals formed during summer fueling denitrification during the subsequent winter. Overall, around 30% of gaseous nitrogen losses in the winter were attributable to autotrophic denitrifiers. To predict long-term nitrogen removal, we developed an electron-transfer model that accounted for the production and consumption of electron donors. The model indicated that the labile organic carbon released from wood chips may be capable of supporting nitrogen removal from wastewater effluent for several decades with sulfide minerals, decaying vegetation, and root exudates likely sustaining nitrogen removal over a longer timescale.

Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling

Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.

Anthropogenic nitrogen pollution in mangrove ecosystems along Dar es Salaam and Bagamoyo coasts in Tanzania

Mangroves are among the most productive coastal ecosystems; however, they are prone to anthropogenic pollution due to their land-sea interface position. We used stable nitrogen isotopes and spectrophotometric nitrate analysis to study the anthropogenic pollution in five mangrove ecosystems in Tanzania, including two polluted (Mzinga and Kizinga), one moderate (Kunduchi) and non-polluted (Mbegani and Ras Dege) sites. Also, we tested the suitability of mangrove leaves, roots, sediment, and gastropod as indicators of anthropogenic nitrogen pollution using stable δ¹⁵N isotope analysis. Results revealed higher than 10‰ δ¹⁵N values in all analysed components and the highest nitrate concentrations of 16.44 mg L^-1 in the interstitial waters at the polluted sites, indicating anthropogenic nitrogen inputs. The δ¹⁵N enrichment increased in the order: non-polluted < moderate < polluted. The polluted sites are fed by freshwater creeks and probably receive high loads of domestic sewage from the surrounding communities, industries, and agricultural effluents. Therefore, to protect mangrove ecosystems, proper waste and wastewater management upstream are recommended.

Macro- and Micronutrient Cycling and Crucial Linkages to Geochemical Processes in Mangrove Ecosystems

High mangrove productivity is sustained by rapid utilization, high retention efficiency and maximum storage of nutrients in leaves, roots, and soils. Rapid microbial transformations and high mineralization efficiencies in tandem with physiological mechanisms conserve scarce nutrients. Macronutrient cycling is interlinked with micronutrient cycling; all nutrient cycles are linked closely to geochemical transformation processes. Mangroves can be N-, P-, Fe-, and Cu-limited; additions of Zn and Mo stimulate early growth until levels above pristine porewater concentrations induce toxicity. Limited nutrient availability is caused by sorption and retention onto iron oxides, clays, and sulfide minerals. Little N is exported as immobilization is the largest transformation process. Mn and S affect N metabolism and photosynthesis via early diagenesis and P availability is coupled to Fe-S redox oscillations. Fe is involved in nitrification, denitrification and anammox, and Mo is involved in NO3− reduction and N2-fixation. Soil Mg, K, Mn, Zn and Ni pool sizes decrease as mangrove primary productivity increases, suggesting increasing uptake and more rapid turnover than in less productive forests. Mangroves may be major contributors to oceanic Mn and Mo cycles, delivering 7.4–12.1 Gmol Mn a−1 to the ocean, which is greater than global riverine input. The global Mo import rate by mangroves corresponds to 15–120% of Mo supply to the oceanic Mo budget.