An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture

Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.

Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance

AIMS

Despite little soil development and organic matter accumulation, lodgepole pine (Pinus contorta var. latifolia) consistently shows vigorous growth on bare gravel substrate of aggregate mining pits in parts of Canadian sub-boreal forests. This study aimed to investigate the bacterial microbiome of lodgepole pine trees growing at an unreclaimed gravel pit in central British Columbia and suggest their potential role in tree growth and survival following mining activity.

METHODS

We characterized the diversity, taxonomic composition, and relative abundance of bacterial communities in rhizosphere and endosphere niches of pine trees regenerating at the gravel pit along with comparing them with a nearby undisturbed forested site using 16S rRNA high-throughput sequencing. Additionally, the soil and plant nutrient contents at both sites were also analyzed.

RESULTS

Although soil N-content at the gravel pit was drastically lower than the forest site, pine tissue N-levels at both sites were identical. Beta-diversity was affected by site and niche-type, signifying that the diversity of bacterial communities harboured by pine trees was different between both sites and among various plant-niches. Bacterial alpha-diversity was comparable at both sites but differed significantly between belowground and aboveground plant-niches. In terms of composition, pine trees predominantly associated with taxa that appear plant-beneficial including phylotypes of Rhizobiaceae, Acetobacteraceae, and Beijerinckiaceae at the gravel pit and Xanthobacteraceae, Acetobacteraceae, Beijerinckiaceae and Acidobacteriaceae at the forest site.

CONCLUSIONS

Our results suggest that, following mining activity, regenerating pine trees recruit bacterial communities that could be plant-beneficial and support pine growth in an otherwise severely N-limited disturbed environment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11104-022-05327-2.

Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria

Lodgepole pine, a prominent Pinaceae tree species native to western North America, is well-known for its ability to thrive in highly disturbed and degraded areas. One such area is the Sub-Boreal Pine-Spruce xeric-cold (SBPSxc) region in British Columbia, Canada, which is characterized by weakly-developed, parched soils that lack an organic forest floor and essential plant-available nutrients. We hypothesized that plant growth-promoting bacteria could play a significant role in sustaining the growth of lodgepole pine trees in the SBPSxc region. Testing this hypothesis, we evaluated plant growth-promoting abilities of six endophytic bacterial strains previously isolated from lodgepole pine trees growing in this region. These bacterial strains significantly enhanced the length and biomass of their natural host (lodgepole pine) as well as a foreign host (hybrid white spruce) in a 540-day long greenhouse trial. This growth stimulation could be linked to the diverse plant growth-promoting (PGP) abilities detected in these strains using in vitro assays for inorganic/organic phosphate-solubilization, siderophore production IAA production, ACC deaminase activity, lytic enzymes (chitinase, β-1,3-glucanase, protease, and cellulase) activity, ammonia production and catalase activity. ACC deaminase activity was also detected in vivo for all strains using ethylene-sensitive plants–canola and tomato. Notably, strains belonging to the Burkholderiaceae family (HP-S1r, LP-R1r and LP-R2r) showed the greatest potential in all PGP assays and enhanced pine and spruce seedling length and biomass by up to 1.5-fold and 4-fold, respectively. Therefore, such bacterial strains with multifarious PGP abilities could be crucial for survival and growth of lodgepole pine trees in the SBPSxc region and could potentially be utilized as bioinoculant for Pinaceae trees in highly disturbed and nutrient-poor ecosystems.

Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites

Lodgepole pine (Pinus contorta var. latifolia) trees have been thriving on unreclaimed gravel mining sites in British Columbia, Canada, with tissue nitrogen-content and growth-rate unaffected by extremely low soil nitrogen-levels. This indicates that pine trees could be accessing a hidden nitrogen source to fulfill their nitrogen requirements – possibly via endophytic nitrogen-fixation. Endophytic bacteria originally isolated from native pine trees growing at gravel sites were selected (n = 14) for in vitro nitrogen-fixation assays and a year long greenhouse study to test the overall hypothesis that naturally occurring endophytic nitrogen-fixing bacteria sustain pine tree growth under nitrogen-limited conditions. Each of the 14 bacteria colonized the internal tissues of pine trees in the greenhouse study and fixed significant amounts of nitrogen from atmosphere (23%–53%) after one year as estimated through 15N isotope dilution assay. Bacterial inoculation also significantly enhanced the length (31%–64%) and biomass (100%–311%) of pine seedlings as compared to the non-inoculated control treatment. In addition, presence of the nifH gene was confirmed in all 14 bacteria. Our results support the possibility that pine trees associate with nitrogen-fixing bacteria, capable of endophytic colonization, to survive at unreclaimed gravel mining pits and this association could potentially be utilized for effective reclamation of highly disturbed sites in a sustainable manner.

Substrate utilization by endophytic bacteria Paenibacillus polymyxa P2b-2R that may facilitate bacterial entrance and survival inside diverse plant hosts

Bacterial endophytes are thought to enter plants either through pre-existing openings in plant tissues or by creating openings by hydrolyzing major plant cell wall components. A lodgepole endophyte, Paenibacillus polymyxa P2b-2R, consistently formed endophytic colonies when inoculated in diverse plant hosts, viz., lodgepole pine, western red cedar, corn, canola, and tomato. We were interested to know, whether or not this bacterial strain possesses enzymes that can hydrolyze three major plant cell wall components namely cellulose, xylan, and pectin to facilitate entrance into the host plants. Using a BIOLOG assay, we also tested this bacterial strain’s ability to utilize carbon sources that might facilitate its entrance and hence its survival inside host plants. Paenibacillus polymyxa P2b-2R hydrolyzed sodium carboxymethylcellulose, beechwood xylan, and sodium polypectate and utilized 39 of the 95 carbon sources (41%) tested. Of the 39 carbon substrates oxidized by P2b-2R, the “carbohydrates” group represents the largest source of utilizable carbon (23 out of 39). Thus, it can be concluded that P. polymyxa P2b-2R is able to degrade major cell wall components (cellulose, xylan, and pectin) and utilize some of the available carbon substrates, possibly to gain entry and survive inside the plant and form endophytic colonies thereafter.