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The microbial communities associated with plant's compartments and the expression of the chloroplast chaperonin Hsp60 have been simultaneously analyzed during the diel cycle in the marine seagrass Thalassia hemprichii from the lagoon of Magoodhoo island (Maldives), characterized by remarkable daily shifts in temperature and light. Plants showed a significant up-regulation of Hsp60 expression from 8.00 a.m. to 2.00 p.m., in correspondence with the increase in temperature and light, confirming their role as defense mechanism against photoinhibition and oxidative damage. However, a further significant increase of the Hsp60 level was also observed when irradiance and temperature dropped, suggesting that the cellular stress was still in progress. The plant-associated microbial communities showed differences by plant compartment and sampling time, with the aboveground compartment (leaves) being much more dynamic than the belowground one (roots/rhizomes). In the phyllosphere, a progressive shift during the day from the absolute dominance of the Gammaproteobacteria class, mainly constituted of Enterobacteraceae family, to the increase of the biodiversity due to the rise of Alphaproteobacteria was observed. Belowground, the microbial diversity was much lower than aboveground, being Gammaproteobacteria the most represented class throughout all sampling times. Vibrionaceae family was the most abundant at 8:00 a.m. and 6.00 p.m. decreasing slightly at 2.00 p.m., partially replaced by Halomonadaceae. The combined biochemical and microbial markers allows to assess the plant stress response and to deepen the knowledge on the seagrasses adaptation to harsh and changing environmental conditions, resulting useful to detect early signs of change in an organism's physiological state. Furthermore, the variation of Hsp60 expression and associated bacterial communities in response to light and temperature fluctuations support the ‘holobiont’ theory, which considers the plant/microorganisms association as a functional unit, as suggested for corals.

Halophila stipulacea is a small tropical seagrass species native to the Red Sea. Due to its invasive character, there is growing interest in understanding its ability to thrive in a broad range of ecological niches. We studied temporal (February 2014 and July 2014), depth (5, 9, 18 m) and spatial (NB and SB) related dynamics of H. stipulacea meadows in the northern Gulf of Aqaba. We evaluated changes in density, morphometry, biomass, and biochemical parameters alongside the reproductive effort. In both sites, maximal growth and vegetative performance occurred in the summer with a marked increase of 35% in shoot density and 18% in biomass; PAR reduction with season and depth induced a significant increase of 28% in leaf area. Sexual reproduction efforts were only observed in July, and the density of plants carrying male or female flowers decreased significantly with depth. The favorable growth responses of H. stipulacea plants observed in the N-enriched NB site suggests their capacity to acclimate to human-disturbed nearshore environments.

Seagrasses are one of the most valuable marine ecosystems on earth, yet they are declining worldwide at alarming rates. With most of seagrass monitoring based on long term responses to environmental pressures, there is growing interest in developing alternative diagnostic tools that more effectively identify changes in seagrass ecological status at an early stage. Besides morphological indicators, functional and biochemical descriptors may provide a good understanding of plant's responses to environmental changes. Moreover, the epiphytic microbial communities of seagrasses may also shift in response to changes in environmental conditions, although these have been seldom used as a descriptor of environmental change. In this study three Halophila stipulacea (Forsk.) Aschers meadows, found in the Gulf of Aqaba (northern Red Sea), were characterized using an integrated approach to highlight possible differences in the meadows ecological status. Plant descriptors, including leaves morphometrics (leaf size, leaf number/plant, leaves with lost apex), photosynthetic pigments (Chlorophylls, Carotenoids) and total phenols contents, were investigated and coupled with the plants’ epiphytic microbial community structure and composition, studied using pyrosequencing. The entire suite of descriptors highlighted differences among the meadows ecological status based on changes in plants’ morphology and biochemistry, and their associated microbial communities, in response to the different environmental conditions (water column turbidity, seawater and sediment nutrients) and the geomorphological features (bottom slope, granulometry) of the stations. Leaf morphology and photosynthetic pigment content were modulated in H. stipulacea in response to light availability and hydrodynamics in the Gulf of Aqaba. The highest leaf surface area and photosynthetic pigment contents were observed at the lowest irradiance and hydrodynamics/granulometry among stations. Total phenol content showed differences among stations with increasing concentrations from north to south. The microbial communities showed differences among stations and plant compartments, with high incidence of Gammaproteobacteria and Bacteroidetes in light limiting conditions, while Cyanobacteria and Rhodobacteraceae thrived in conditions of high light availability and hydrodynamics. The mutual response of the seagrass plants and the microbial communities provided evidence of their functional relationship, which undoubtedly needs further investigation. To the best of our knowledge, this is the first time that such descriptors have been used in an integrated approach. We provide evidence of their effectiveness in discriminating seagrass ecological status, even at small spatial scales. This work constitutes a new approach to the assessment of seagrasses and a stepping stone in the application of microbial communities as a putative marker in a changing environment.

Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1–50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species’ capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4–28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4–28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.

Ancient parchments are commonly attacked by microbes, producing purple spots and detachment of the superficial layer. Neither standard cultivation nor molecular methods (DGGE) solved the issue: causative agents and colonization model are still unknown. To identify the putative causal agents, we describe the 16 S rRNA gene analysis (454-pyrosequencing) of the microbial communities colonizing a damaged parchment roll dated 1244 A.D. (A.A. Arm. I-XVIII 3328, Vatican Secret Archives). The taxa in damaged or undamaged areas of the same document were different. In the purple spots, marine halotolerant Gammaproteobacteria, mainly Vibrio, were found; these microorganisms are rare or absent in the undamaged areas. Ubiquitous and environmental microorganisms were observed in samples from both damaged and undamaged areas. Pseudonocardiales were the most common, representing the main colonizers of undamaged areas. We hypothesize a successional model of biodeterioration, based on metagenomic data and spectroscopic analysis of pigments, which help to relate the damage to a microbial agent. Furthermore, a new method (Light Transmitted Analysis) was utilized to evaluate the kind and entity of the damage to native collagen. These data give a significant advance to the knowledge in the field and open new perspectives to remediation activity on a huge amount of ancient document.

Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1–50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species’ capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4–28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4–28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.

Tropical coastal marine systems inhabited by macroalgae can typically be categorized as coral reefs, seagrass meadows, or mangrove forests. The role of macroalgae in these systems is fundamentally different from temperate systems, as other primary producers generally act as the dominant habitat providers. However, macroalgae do provide essential ecosystem services such as the reduction of nutrients, provision of food, and spatial refuge for predator and prey alike. In seagrass beds, they can be highly productive and may help to stabilize pH levels. Their role within mangrove systems is highly variable across regions and their contribution to trophic food webs and nutrient cycling is likely significant. Through competition and grazing, the biomass of macroalgae is reduced in most healthy tropical ecosystems. Macroalgae are a critical component of healthy tropical marine habitats; however, their unchecked growth can lead to complete regime shifts, thereby threatening the stability and welfare of the entire coastal system.