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

Abstract

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.

Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing

“…In contrast, intraspecific variation involves differences between microbiomes that are associated with different host genotypes or across the biogeographical range of the same species. Both types of variation have been previously reported for seagrass [40,41], mangrove [42,43], and saltmarsh [44][45][46][47] microbiomes, with a focus on each habitat separately. By addressing this question, we may be able to establish generalised patterns of both types of microbial change within and among the three habitats.…”

Microbiome transfer from native to invasive species may increase invasion risk and shorten invasion lag

“…The number of studies comparing the microbiome of native and invasive species in plants is growing rapidly (Coats and Rumpho, 2014; Aires et al, 2021), but only a few studies have focused on comparing the microbiome of native and invasive animals (Chiarello et al, 2022; Santos et al, 2021). In a recent study, Chiarello et al (2022) found that native mussels shared a substantial fraction of their microbiome with the co-occurring invasive species Corbicula fluminea , indicating that invasive mussels may host microbial communities that are obtained locally.…”

Divergence of epibacterial community assemblage correlates with malformation disease severity in Saccharina japonica seedlings

“…The extracted DNA was assessed by gel electrophoresis, and the qualified DNA was then stored at −20°C until used for amplification. To preclude amplification of plastid sequences, the primers 799F and 1193R were used to amplify the V5-V7 hypervariable regions of the 16S rRNA gene which has been used in the study of plants and algae microbiota (Zhang et al, 2019;Aires et al, 2021). The amplicon libraries were constructed using TruSeq Nano DNA LT Library Prep Kit (Illumina, San Diego, CA, USA), following the manufacturer's recommendations, and index codes were added.…”