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

Disturbance of primary producer communities disrupts the thermal limits of the associated aquatic fauna

Environmental fluctuation forms a framework of variability within which species have evolved. Environmental fluctuation includes predictability, such as diel cycles of aquatic oxygen fluctuation driven by primary producers. Oxygen availability and fluctuation shape the physiological responses of aquatic animals to warming, so that, in theory, oxygen fluctuation could influence their thermal ecology. We describe annual oxygen variability in agricultural drainage channels and show that disruption of oxygen fluctuation through dredging of plants reduces the thermal tolerance of freshwater animals. We compared the temperature responses of snails, amphipods, leeches and mussels exposed to either natural oxygen fluctuation or constant oxygen in situ under different acclimation periods. Oxygen saturation in channel water ranged from c. 0 % saturation at night to >300 % during the day. Temperature showed normal seasonal variation and was almost synchronous with daily oxygen fluctuation. A dredging event in 2020 dramatically reduced dissolved oxygen variability and the correlation between oxygen and temperature was lost. The tolerance of invertebrates to thermal stress was significantly lower when natural fluctuation in oxygen availability was reduced and decoupled from temperature. This highlights the importance of natural cycles of variability and the need to include finer scale effects, including indirect biological effects, in modelling the ecosystem-level consequences of climate change. Furthermore, restoration and management of primary producers in aquatic habitats could be important to improve the thermal protection of aquatic invertebrates and their resistance to environmental variation imposed by climate change

<em>Mangrovimonas cancribranchiae</em> sp. nov., a novel bacterial species associated with the gills of the fiddler crab <em>Cranuca inversa</em> (Brachyura, Ocypodidae) from Red Sea mangroves

\ua9 2024 The Authors. Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20–37 \ub0C (optimum, 28–35 \ub0C), at pH 5.0–9.0 (optimum, pH 6.0–7.0), and with 1–11 % (w/v) NaCl (optimum, 2–4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA–DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15: 0 and iso-C15: 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T)

Comunità microbica associata a Hyalesthes obsoletus Signoret, vettore del Legno nero della vite

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Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10?MPa, corresponding to a depth of 0, 500 and 1000?m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10?MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10?MPa CO2 production per cell was not affected, cell integrity was preserved and PO43- uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential

Study of the bacterial community affiliated to Hyalesthes obsoletus, the insect vector of “bois noir” phytoplasma of grape

Grape yellows caused by phytoplasmas afflict several important wine-producing areas of Europe. A grape yellows with increasingincidence in European vineyards is “bois noir” (BN), caused by ‘Candidatus Phytoplasma solani’. Its vector is the planthopperHyalesthes obsoletus Signoret (Hemiptera Cixiidae), occasionally feeding on grapevine. An innovative strategy for reducing thediffusion of the disease could be symbiotic control, exploiting the action of symbiotic microorganisms of the insect host. To investigatethe occurrence of possible microbial candidates for symbiotic control we performed a molecular characterization of thebacteria associated to H. obsoletus. Length heterogeneity PCR was applied for a preliminary population screening. Taxonomicaffiliations of the bacterial species were analyzed by denaturing gradient gel electrophoresis, showing, within the microbial diversity,the intracellular reproductive parasite Wolbachia pipientis and a Bacteroidetes symbiont with 92% nt identity with ‘CandidatusSulcia muelleri’. PCR essays specific for these bacteria showed they co-localize in several organs of H. obsoletus. Fluorescentin situ hybridization was performed to assess the distribution of these microorganisms within the insect body, showing interestinglocalization patterns, particularly in insect gonads and salivary glands. These results could be a starting point for a deeper investigationof functions and relationships between microbial species

16S-23S rRNA intergenic spacer region sequence variation in Streptococcus thermophilus and related dairy streptococci and development of a multiplex ITS-SSCP analysis for their identification

The 16S-23S rRNA internal transcribed spacer (ITS) region of several Streptococcus thermophilus strains and some related dairy streptococci, S. macedonicus, S. salivarius and S. bovis, was analysed by sequence analysis. All the Streptococcus species were easily discriminated on the basis of sequence variations principally located upstream and downstream of the region encompassing the double-stranded processing sites and the tRNA(Ala) gene. Comparison between tRNA(Ala) gene sequences highlighted a high level of sequence conservation among the Streptococcus species investigated despite their belonging to separated phylogenetic clusters, i.e. the S. salivarius and S. bovis rRNA groups. A low but significant degree of variability was detected among the S. thermophilus strains, allowing the identification of four different ITS sequences. Similarity analysis of the ITS sequences showed that the Streptococcus species were clustered in two main branches, one containing S. macedonicus and S. bovis strains, and one containing S. thermlophilus and S. salivarius strains. With the aim of developing a rapid tool for the identification of the dairy streptococci species a multiplex ITS-SSCP analysis of two discrete regions within the ITS locus was carried out

Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities

ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the fac\ub8ade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxic basin in the Mediterranean Sea were analyzed with the three primer sets. The number of peaks in the ARISA profiles, the range of peak size (width of the profile), and the reproducibility of results were used as indices to evaluate the efficiency of the three primer sets. The overall data showed that ITSF and ITSReub generated the most informative (in term of peak number) and reproducible profiles and yielded a wider range of spacer sizes (134 to 1,387) than the other primer sets, which were limited in detecting long fragments. The minimum amount of DNA template and sensitivity in detection of minor DNA populations were evaluated with artificial mixtures of defined bacterial species. ITSF and ITSReub amplified all the bacteria at DNA template concentrations from 280 to 0.14 ng l 1, while the other primer sets failed to detect the spacers of one or more bacterial strains. Although the primer set consisting of ITSF and ITSReub and that of S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 showed similar sensitivities for the DNA of Allorhizobium undicula mixed with the DNA of other species, the S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 primer set failed to detect the DNA of Pseudomonas stutzeri

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.Versión del edito

Disturbance of primary producer communities disrupts the thermal limits of the associated aquatic fauna

Environmental fluctuation forms a framework of variability within which species have evolved. Environmental fluctuation includes predictability, such as diel cycles of aquatic oxygen fluctuation driven by primary producers. Oxygen availability and fluctuation shape the physiological responses of aquatic animals to warming, so that, in theory, oxygen fluctuation could influence their thermal ecology. We describe annual oxygen variability in agricultural drainage channels and show that disruption of oxygen fluctuation through dredging of plants reduces the thermal tolerance of freshwater animals. We compared the temperature responses of snails, amphipods, leeches and mussels exposed to either natural oxygen fluctuation or constant oxygen in situ under different acclimation periods. Oxygen saturation in channel water ranged from c. 0 % saturation at night to >300 % during the day. Temperature showed normal seasonal variation and was almost synchronous with daily oxygen fluctuation. A dredging event in 2020 dramatically reduced dissolved oxygen variability and the correlation between oxygen and temperature was lost. The tolerance of invertebrates to thermal stress was significantly lower when natural fluctuation in oxygen availability was reduced and decoupled from temperature. This highlights the importance of natural cycles of variability and the need to include finer scale effects, including indirect biological effects, in modelling the ecosystem-level consequences of climate change. Furthermore, restoration and management of primary producers in aquatic habitats could be important to improve the thermal protection of aquatic invertebrates and their resistance to environmental variation imposed by climate change