Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms

Impact of persistently high sea surface temperatures on the rhizobiomes of Zostera marina in a Baltic Sea benthocosms

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass-microorganism interactions is needed to leverage knowledge on host-microbe interactions in seagrasses.

Microbiomes of Thalassia testudinum throughout the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico are influenced by site and region while maintaining a core microbiome

Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.

Sediment carbon storage differs in native and non-native Caribbean seagrass beds

Non-native species are expanding globally and can alter ecosystem functions, including food web dynamics, community structure and carbon storage. Seagrass are foundation species that contribute a variety of ecosystem services in near-shore coastal ecosystems, including a significant sink of carbon. In the Caribbean, the rapidly expanding non-native Halophila stipulacea has unknown impacts on carbon storage. To investigate the impacts on carbon storage, we quantified organic carbon (Corg) content in sediment and seagrass tissues from monotypic H. stipulacea beds, mixed native seagrass beds dominated by Thalassia testudinum and Syringodium filiforme, and unvegetated substrate in St. John, USVI. We found native seagrass-vegetated sediment contained 1.3 times more Corg than sediment covered by H. stipulacea, and 1.6 times more Corg than unvegetated areas on average. Whereas, H. stipulacea-dominated substrate stored 1.2 times more Corg than unvegetated substrate. Likewise, native species contained 2.2 times more aboveground biomass and 6.0 times more belowground biomass than H. stipulacea. Since seagrasses are critical sources of carbon sequestration, our results suggest that invading H. stipulacea is associated with lower carbon stocks which has potential implications for conservation activities and climate change mitigation.

Ecotoxic side-effects of allelochemicals on submerged plant and its associated microfloras effectively relieved by sustained-release microspheres

Harmful algae bloom caused by water eutrophication is a burning question worldwide. Allelochemicals sustained-release microspheres (ACs-SMs) exhibited remarkable inhibition effect on algae, however, few studies have focused on the ecotoxic side-effects of ACs-SMs on submerged plant and its associated microfloras. Herein the effects of different exposure situations including single high-concentration ACs (15 mg/L, SH-ACs), repeated low-concentration ACs (3 × 5 mg/L, RL-ACs) and ACs-SMs containing 15 mg/L ACs on morphological indexes, chlorophyll content, lipid peroxidation, enzymatic activity, and chlorophyll fluorescence indexes of submerged plant Vallisneria natans and the richness and diversity of its associated microfloras (epibiotic microbes and sediment microbes) were studied. The results showed that pure ACs (RL-ACs and SH-ACs groups) had negative effects on plant height, mean leaf number and area of V. natans, but promoted the increase of mean leaf length. In addition, pure ACs caused lipid peroxidation, activated the antioxidant defense system, decreased chlorophyll content, and damaged photosynthetic system in leaves. Interestingly, ACs-SMs not only had barely negative effects on above indexes of V. natans, but had certain positive effects at the later experiment stage (days 50-60). Pure ACs and ACs-SMs all reduced the richness and diversity of microfloras in each group, and promoted the increase of relative abundance of dominant bacteria Pseudomonas, leading to a simpler community structure. Significantly, V. natans leaves diminished the effects of pure ACs and ACs-SMs on epibiotic microbes, and the plant rhizosphere was beneficial to the increase of dominant bacteria that promoted plant growth. Thus, sustained-release microspherification technology can effectively relieve the ecotoxic side-effects of pure ACs on submerged plant and its associated microfloras. This study fills the gap on the ecological safety knowledge of ACs-SMs and provides primary data for evaluating the feasibility and commercialization prospects of ACs-SMs as algae inhibitor in aquatic ecosystem.

A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations

Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.

[Gut microbiota and chronic inflammatory bowel disease]

Intestinal dysbiosis remains the focus of research into the pathogenesis of chronic inflammatory bowel disease (IBD). The potential role of gut microbiota in the development of IBD includes interaction with the host genome and immune system, as well as various environmental factors, diet, drugs, industrialization, etc. Other organs are negatively affected by intestinal dysbiosis via gut-brain axis. The composition of microbiota and its metabolic activity has a significant impact on the effectiveness of anti-inflammatory therapies. Microbiome-based treatment for IBD includes the use of diet, antibiotics, pre-, pro- and synbiotics, and faecal transplantation (FMT). The development of effective therapies for IBD patients will only be possible once the interactions between the microbiota and its metabolites and the host immune system are better understood.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.