Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

Abstract

Climate change directly affecting the Antarctic Peninsula has been reported to induce the successful colonization of ice-free lands by two Antarctic vascular plants (Deschampsia antarctica and Colobanthus quitensis). While studies have revealed the importance of microbiota for plant growth and stress tolerance in temperate climates, the role that plant-associated microbes play in the colonization of ice-free lands remains unknown. Consequently, we used high-throughput DNA sequence analyses to explore the composition, predicted functions, and interactive networks of plant-associated microbial communities among the rhizosphere, endosphere, and phyllosphere niches of D. antarctica and C. quitensis. Here we report a greater number of operational taxonomic units (OTUs), diversity, and richness in the microbial communities from the rhizosphere, relative to endosphere and phyllosphere. While taxonomic assignments showed greater relative abundances of Proteobacteria, Bacteroidetes, and Actinobacteria in plant niches, principal coordinate analysis revealed differences among the bacterial communities from the other compartments examined. More importantly, however, our results showed that most of OTUs were exclusively found in each plant niche. Major predicted functional groups of these microbiota were attributed to heterotrophy, aerobic heterotrophy, fermentation, and nitrate reduction, independent of plant niches or plant species. Co-occurrences network analyses identified 5 (e.g., Microbacteriaceae, Pseudomonaceae, Lactobacillaceae, and Corynebacteriaceae), 23 (e.g., Chitinophagaceae and Sphingomonadaceae) and 7 (e.g., Rhodospirillaceae) putative keystone taxa present in endosphere, phyllosphere, and rhizosphere, respectively. Our results revealed niche differentiation in Antarctic vascular plants, highlighting some putative microbial indicators and keystone taxa in each niche. However, more studies are required to determine the pivotal role that these microbes play in the successful colonization of ice-free lands by Antarctic plants.

Isolation and Characterization of Cold-Tolerant Hyper-ACC-Degrading Bacteria from the Rhizosphere, Endosphere, and Phyllosphere of Antarctic Vascular Plants

“…Because bacterial communities associated with native plants grown in Antarctic ecosystems have coevolved with their plant hosts and local conditions, they may exhibit a wide variety of metabolic features that contribute to the adaptation of plants to nutrient-poor soils and harsh conditions. In this regard, the results of a number of studies have revealed a compartmentalization of the structure and functionality of bacterial communities in the different niches of D. antarctica and C. quitensis , where the occurrence of plant growth-promoting (PGP) bacteria can occur, influencing the tolerance of plants to abiotic stresses [ 25 , 29 , 30 ]. Studies have also demonstrated that plants under stress conditions produce and concentrate ACC in their tissues [ 31 , 32 ], which may result in an increased density of active ACC-degrading bacteria with a simultaneous decrease in the ACC concentration in the plant tissues [ 33 ].…”

“…Regarding the taxonomic affiliation of cold-tolerant hyper-ACC degrading bacteria, 5 of 12 isolates were affiliated with the Pseudomonas genus, members of which have been described as a common inhabitants of Antarctic plant roots [ 38 , 40 , 53 ]. A recent metagenomic study revealed that Pseudomonadaceae was the most abundant family in the endosphere and phyllosphere samples of D. antarctica and C. quitensis [ 25 ]. Similarly, Cid et al [ 18 ] observed Pseudomonas as the predominant genus in the phyllosphere of D. antarctica .…”

“…Sampling was performed as previously described by [ 25 ]. Briefly, specimens of D. antarctica and C. quitensis ( Figure 1 a,b) and their respective rhizosphere soils were collected from mantles located at the South Shetland Islands (62°59′53″ S, 60°35′17″ W and 62°24′7″ S, 58°18′29″ W, respectively) during Antarctic Scientific Expedition no.…”

Rice Root-Associated Diazotrophic Community Succession is Driven by Growth Period Combined With Fertilization

“…Habitat heterogeneity in uenced the bacterial [69] and fungal [70] network interactions. In our work, rhizosphere diazotrophs formed larger and more complex networks than endophytic diazotrophs at the DNA and RNA levels.…”

Diversity, Interaction, and Bioprospecting of Plant-Associated Microbiomes

“…Omic studies have suggested that certain keystone taxa or key phylotypes govern the networking interactions between community members, expanding our knowledge about how microbes adapt to the plant's environmental pressures [6]. The occurrence of those microbial indicators or key taxa has been reported in a wide range of samples of planted soil [7] and plant compartments (rhizosphere, endosphere, and phyllosphere) [8], as well as in plants grown in agricultural soils or extreme environments [9,10]. However, the molecular mechanisms that modulate these plant-microbe selections and interactions are still poorly understood at the community level; thus, deeper studies are highly required.…”