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

The Fungal Development During The Leaf Litter Process Decomposition of Avicennia marina

The existence of mangrove ecosystems decreases from land conversion into residential areas, industries, plantations, road facilities and the construction of ponds. This research was conducted in the mangrove forest area of Secanang Belawan Village, Medan, at the Biotechnology Laboratory of the Department of Forestry, Faculty of Agriculture, USU and at the Microbiology Laboratory, Department of Biology, Faculty of Mathematics and Natural Sciences, USU Medan. The study's objective was to identify the different fungal species that were present at 10 ppt salinity levels, 10–20 ppt, and 20–30 ppt as well as the pace at which Avicennia marina leaf litter. The research method used litter bags filled with leaf litter of Avicennia marina (50 g) with 7 treatments, 3 replications and 3 levels of salinity. The A. marina leaf litter that had a salt level of 10 ppt had the highest level of decomposition. The dry weight of leaf litter left in the litter bag, which is 4.92 g on average. The largest dry weight of the remaining litter was found in an environment with a salinity of 20 – 30 ppt, which is an average of 10.42 g. The rate of decomposition of A. marina leaf litter in an environment with a salt level greater than 30 ppt is 6.53/yr (or almost equal to residence period of = 0.15 yr). The number of fungal species discovered in the leaf litter of A. marina, which goes through a breakdown process at salinity levels between 0 and 10 ppt and contains 9 species, is another way to observe the impact of salt level. In comparison to the large at salinity levels of 10 to 20 ppt and 20 to 30 ppt, respectively, there were populations of fungus that underwent the process of decomposition in A. marina leaf litter, with an average of 5.99 x 102 cfu/ml and 5.5 x 102 cfu/ml, the fungal population that was the highest concentration was 10.72 x 102 cfu/m

The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature‐based solutions for mangroves

Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a ‘halo effect’, can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services

MANGROVE GROWTH PROMOTION BY ENDOPHYTIC ACTINOBACTERIA AND SEAWEED EXTRACT

In this study, I aimed to determine the impact of the application of a commercial seaweed extract (SWE) bio-stimulant and endophytic actinobacterial isolates on growth performance and endogenous hormonal levels of mangroves. Therefore, I isolated endophytic plant growth promoting (PGP) actinobacteria (PGPA) from mangrove roots; and evaluated their potential as biological inoculants on mangrove seedlings under greenhouse and open-field nursery conditions. Seven salt tolerant isolates had the ability to produce different levels of in vitro plant growth regulators (PGRs) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD), and to solubilize phosphorus. Accordingly, only one isolate, Streptomyces tubercidicus UAE1 (St), was selected based on its relative superiority in displaying multiple modes of action and in successfully colonizing mangrove tissues for 15 weeks. In the greenhouse experiments, plants treated with either St or SWE significantly (P\u3c0.05) improved dry biomass by 40.2 and 55.1% in roots and 42.2 and 55.4% in shoots, respectively compared to seawater-irrigated non-treated mangrove plants (control). However, St+SWE caused a greater significant (P\u3c0.05) increase in dry weight of roots (67.6%) and shoots (65.7%) than control plants. Following the combined treatment of St+SWE, in planta PGR levels were found to be greatly enhanced over the non-treated control or treated plants grown in sediments inoculated with St or supplied with SWE only. This was evident from the significant (P\u3c0.05) increases in the photosynthetic pigments and production of PGRs, as well as the reduction in the endogenous ACC levels of plant tissues compared to those in other treatments. Tissue nutrient contents of seedlings also increased by at least two-fold in St+SWE treatment compared to control. Similar effects were observed on all growth parameters under natural open-field nursery conditions. This report is the first in the field of marine agriculture that uses SWE as a nutrient base for actinobacteria capable of producing PGRs and ACCD. By combining St with SWE, this does not only stimulate plant growth but also potentially has additive effects on mangrove ecosystem productivity in nutrient-impoverished soils in the Arabian coastal areas

Fungal succession on the decomposition of three plant species from a Brazilian mangrove.

Abstract: Leaf decomposition is the primary process in release of nutrients in the dynamic mangrove habitat, supporting the ecosystem food webs. On most environments, fungi are an essential part of this process. However, due to the peculiarities of mangrove forests, this group is currently neglected. Thus, this study tests the hypothesis that fungal communities display a specific succession pattern in different mangrove species and this due to differences in their ecological role. A molecular approach was employed to investigate the dynamics of the fungal community during the decomposition of three common plant species (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) from a mangrove habitat located at the southeast of Brazil. Plant material was the primary driver of fungi communities, but time also was marginally significant for the process, and evident changes in the fungal community during the decomposition process were observed. The five most abundant classes common to all the three plant species were Saccharomycetes, Sordariomycetes, Tremellomycetes, Eurotiomycetes, and Dothideomycetes, all belonging to the Phylum Ascomycota. Microbotryomycetes class were shared only by A. schaueriana and L. racemosa, while Agaricomycetes class were shared by L. racemosa and R. mangle. The class Glomeromycetes were shared by A. schaueriana and R. mangle. The analysis of the core microbiome showed that Saccharomycetes was the most abundant class. In the variable community, Sordariomycetes was the most abundant one, mainly in the Laguncularia racemosa plant. The results presented in this work shows a specialization of the fungal community regarding plant material during litter decomposition which might be related to the different chemical composition and rate of degradation

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds

Fungal Endophytes Isolated From Mangroves In San Pedro Nature Reserve, Buenaventura

Mangroves offer a variety of economic, ecological, and cultural services. However, despite their importance and the diversity they harbor, anthropogenic activities have contributed to the deterioration of these habitats. Studies on endophytic fungi associated with mangrove ecosystems are still limited in Colombia. This group of fungi includes a wide variety of opportunistic pathogens often associated with trees affected by environmental and anthropogenic activities. To contribute to the knowledge of the diversity of endophytic fungi associated with mangrove trees in San Pedro Nature Reserve, Buenaventura, Colombia, branches (aprox. 10 cm length) of Laguncularia racemosa, Mora oleifera, Pelliciera rhizophorae and Rhizophora racemosa were collected for fungal isolations. The DNA was extracted and the Internal Transcribed Spacer region was amplified followed by the subsequent phylogenetic analyzes of Bayesian, maximum likelihood, and maximum parsimony. Nine genera, Bipolaris, Ciboria, Coprinellus, Cylindrobasidium, Epicoccum, Fusarium, Lasiodiplodia, Neofusicoccum and Neurospora belonging to eight families, were recognized. Of these, Fusarium, Lasiodiplodia, Neofusicoccum are well known for their high potential to threaten the health of their hosts. Results suggest that mangroves constitute an environment that has hardly been explored for the study of different groups of fungi

Molecular identification of fungi isolated from coastal regions of Red Sea, Jeddah, Saudi Arabia

AbstractTo isolate fungal communities from coastal areas of the Red Sea in Saudi Arabia and identify and classify them by molecular techniques. Samples were collected from the seaside of the Red Sea in Jeddah, Saudi Arabia during March 2012 and stored in sterile screw cap bottles for further analysis. Phenotypic and genotypic characterization of fungal isolates were done using standard techniques. Eight fungal genera including Aspergillus, Penicillium, Thielavia, Fusarium, Emericella, Cladosporium, Scytalidium and Alternaria. Most isolated fungi showed significant growth on petroleum media and were thus considered capable of biodegradation of crude oil based substances. The fungal genera isolated from the Red Sea had 97–100% similarity with the related fungi recorded in the GenBank in which they were deposited. The morphological and molecular structure of these marine fungal isolates closely resembles their terrestrial counterparts in the GenBank. The capabilities of these fungal species to utilize petroleum as a source of carbon speaks to future applications in which marine fungi may be utilized in the breakdown of petroleum-based waste in an ecologically efficient manner

Characterization and phylogeny of fungi isolated from industrial wastewater using multiple genes

The aim of this study was the isolation and molecular characterization of fungi from untreated refinery effluent by using multiple conserved genes. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM), and RNA polymerase second large subunit (RPB2) genes, along with morphological characterization. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium, and Trichoderma with Aspergillus as the predominant genus were identified. Therefore these genes should be used as molecular markers for species level identification of fungi (especially Aspergillus and Penicillium as proven in this study

Genetic insights into climate-driven range expansion of a coastal foundation species

In this thesis, I address gaps in our understanding of how climate-driven range expansion can shape genetic variation within a coastal foundation species and how the resulting genetic changes may have broader ecological consequences. To do this, I study the neotropical black mangrove (Avicennia germinans) across its distribution in the United States, and then I focus on its expanding Atlantic Florida range margin. First, in Chapter 2, I find that genetic variation within A. germinans declines towards three range margins in the United States, but that this reduction may not constrain adaptation within this species as range-margin A. germinans exhibit shifts in functional traits consistent with greater cold tolerance. Leveraging these insights and genetic data, I then document patterns in mating system and dispersal, factors that can shape intraspecific genetic variation and influence expansion success, towards the Atlantic Florida range margin. In Chapter 3, I find evidence for plastic shifts towards greater self-fertilisation at this sparsely-populated range margin, a mechanism that can facilitate colonisation of new areas. In Chapter 4, I show how extreme storm events may facilitate poleward expansion of A. germinans and how this form of episodic dispersal can shape genetic variation within newly-colonised populations. Finally, I evaluate potential ecological consequences of the unique genetic variation found within these Atlantic Florida A. germinans. In Chapter 5, at the scale of a range-margin population, I find that genetically-similar A. germinans harboured similar fungal communities, a relationship that may have implications for the fitness of these mangrove hosts. In Chapter 6, using a greenhouse common garden, I demonstrate a genetic basis to adaptative trait shifts within these range-margin A. germinans that may facilitate future range expansion of this species. These novel insights should improve our ability to predict how mangrove range margins may respond to climate change and help inform future mangrove restoration initiatives