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Mangrove endophytic fungi can produce impressive quantities of metabolites with promising antioxidant activities that may be useful to humans as novel physiological agents. In this study, we investigated the phylogenetic diversity and antioxidant potential of 46 fungal endophytes derived from the mangrove species Rhizophora stylosa and R. mucronata from the South China Sea. The fungal isolates were identified using a combination of morphological characteristics and phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Seventeen genera belonging to 8 taxonomic orders of Ascomycota were discovered, specifically, Botryosphaeriales, Capnodiales, Diaporthales, Eurotiales, Glomerellales, Hypocreales, Pleosporales, and Xylariales. The most abundant fungal orders included Xylariales (35.49%) and Diaporthales (27.61%), which were predominantly represented by the culturable species Pestalotiopsis sp. (34.54%) and Diaporthe sp. (18.62%). The stems showed more frequent colonization and species diversity than the roots, leaves, hypocotyls, and flower tissues of the host plant. The antioxidant activities of all the isolated fungal extracts on four different culture media were assessed using improved 2,2'-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonicacid) (ABTS) methods. A relatively high proportion (84.8%) of the isolates displayed antioxidant capacity (%RSA > 50%). Further research also provided the first evidence that HQD-6 could produce flufuran as a significant radical scavenger with IC50 values of 34.85±1.56 and 9.75±0.58 μg/mL, respectively. Our findings suggest that the utilization of a biotope such as that of the endophytic fungal community thriving on the mangrove plants R. stylosa and R. mucronata may be suitable for use as a sustainable resource for natural antioxidants.

Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.

To elucidate the physiological and molecular mechanisms underlying cold tolerance in the mangrove species Kandelia obovata Sheue & al, this study measured the antioxidant enzyme activities and photosynthetic pigment contents of two populations—cold-tolerant and -sensitive—under natural overwintering conditions. In addition, transcriptome sequencing was performed to analyze differentially expressed genes (DEGs), transcription factor families, single nucleotide polymorphisms (SNPs), and alternative splicing events. The results showed that catalase activity was significantly elevated in the cold-tolerant population, which enhanced the efficiency of hydrogen peroxide scavenging. In contrast, although the superoxide dismutase activity was relatively high in the cold-sensitive population, its downstream scavenging capacity was insufficient, resulting in an overall lower antioxidant efficiency. The KEGG enrichment analysis indicated that pathways such as phenylpropanoid biosynthesis, amino sugar metabolism, and plant hormone signal transduction might be involved in the response to low-temperature stress. Further analysis revealed that transcription factors such as WRKY, NAC, MYB, and ERF were differentially expressed at significant levels in the cold-tolerant population, suggesting that they may play important roles in low-temperature adaptation. In addition, the diversity of SNPs and alternative splicing events may enhance protein function and contribute to improved cold tolerance. In summary, the cold-tolerant K. obovata population achieves low-temperature tolerance through multiple mechanisms, including antioxidant defense, metabolic regulation, and transcriptional as well as post-transcriptional regulation. This study provides a theoretical basis for elucidating the molecular foundations of cold tolerance in K. obovata.

Endogenous melatonin (MEL) and abscisic acid (ABA) are involved in the adaptation of plants to environmental stresses. The application of exogenous serotonin (SER) to plants can enhance their tolerance to abiotic stress, such as cold. However, the mechanism associated with serotonin-mediated defense against cold-induced damage in mangroves is still poorly understood. In this study, we demonstrated that mangrove (Kandelia obovata) seedlings sprayed with 200 μmol·L−1 serotonin exhibited enhanced cold tolerance, as shown by reduced damage to leaves and loss of photosynthesis when exposed to low-temperature conditions. The mechanism associated with the cold adaptation of K. obovata seedlings upon treatment with serotonin was subsequently investigated by transcriptomic analysis. Serotonin treatment caused changes in differentially expressed genes (DEGs) involved in the regulation of melatonin (MEL) and ABA biosynthesis and defense responses against cold stress. Under low-temperature stress, serotonin-treated seedlings showed a significant increase in the endogenous levels of melatonin and ABA. By contrast, under normal growth conditions, K. obovata seedlings treated with serotonin displayed no substantial change in melatonin level, whereas ABA level significantly increased. These findings demonstrated that serotonin treatment might play an important role in the enhanced resistance to cold in K. obovata and that such an effect would depend on the activation of endogenous melatonin and ABA synthesis.

• Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. • We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. • The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. • The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.

The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves ( Rhizophora mangle ) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher F ST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.

Abstract Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray–Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling. We explored the bacterial microbiome of red mangrove trees and found significant variation across tissue types and host populations.

Climatic oscillations during the Pleistocene played a major role in shaping the spatial distribution and demographic dynamics of Earth’s biota, including our own species. The Last Interglacial (LIG) or Eemian Period (ca. 130 to 115 thousand years B.P.) was particularly influential because this period of peak warmth led to the retreat of all ice sheets with concomitant changes in global sea level. The impact of these strong environmental changes on the spatial distribution of marine and terrestrial ecosystems was severe as revealed by fossil data and paleogeographic modeling. Here, we report the occurrence of an extant, inland mangrove ecosystem and demonstrate that it is a relict of the LIG. This ecosystem is currently confined to the banks of the freshwater San Pedro Mártir River in the interior of the Mexico–Guatemala El Petén rainforests, 170 km away from the nearest ocean coast but showing the plant composition and physiognomy typical of a coastal lagoon ecosystem. Integrating genomic, geologic, and floristic data with sea level modeling, we present evidence that this inland ecosystem reached its current location during the LIG and has persisted there in isolation ever since the oceans receded during the Wisconsin glaciation. Our study provides a snapshot of the Pleistocene peak warmth and reveals biotic evidence that sea levels substantially influenced landscapes and species ranges in the tropics during this period.

Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R.  ×  selala . The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia, and other stressors in the new habitat might have affected both genomic features and protein structures. Here, we developed a new method for detecting convergence at conservative Sites (CCS) and applied it to the genomic sequences of mangroves. In simulations, the CCS method drastically reduces random convergence at rapidly evolving sites as well as falsely inferred convergence caused by the misinferences of the ancestral character. In mangrove genomes, we estimated ∼400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives. The convergent genes are enriched in pathways related to stress response and embryo development, which could be important for mangroves’ adaptation to the new habitat.