Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

Shifts in climate along elevation gradients structure mycobiont–photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora s.lat., Bryonora, Myriolecis, Protoparmeliopsis, the “Lecanora” polytropa group, and the “L.” saligna group. All of these clades except for Lecanora s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

Developing nation’s soil microbial community shifts and diversity loss: leading towards major ecological threat

Nature does not discriminate and has no boundaries; however only developing nations faces huge food security issues and in such circumstances much of importance has been emphasised on food production technologies but studies and research on concealed factor behind food production i.e biogeochemical drivers were largely overlooked. Injudicious agricultural practices; for instance profound use of agrochemicals in continuous and unmonitored way may had already situate many soil microbial species in verge of extinction consequently creating ecological imbalance. With huge land pressure for crop production and lack of upto date technologies of preciseness, most of the developing nation which includes the whole of Africa, almost all Asian countries and numerous other island states faces the agricultural land degradation issues; one of the major reason for such degradation is missing out of ecological drivers i.e soil microbial diversity. Anthropogenic activities application of fertilisers, land use changes (LUC), land intensification, crop diversification, irrigation management etc accelerates the soil microbial community shifts and microbial diversity loss predominately in developing nations. In this short communication, we address the concerns faced by the developing nations to prevent the soil microbial community shift and diversity loss. Also we propose the each exported commodity may have specific tax included which may be utilised by soil scientist from developing nations for studying the current soil microbial shifts and diversity loss due to agriculture management practices more efficiently.

Characterising the benthic Phormidium autumnale-dominated biofilm community and anatoxin production throughout biofilm succession

<p>There has been an increase in the prevalence and intensity of Phormidium autumnale-dominated benthic blooms in New Zealand over the last decade. This species produces the potent neurotoxins Anatoxin-a, Homoanatoxin-a and their derivatives, and consumption of P. autumnale biofilms has led to over 70 dog deaths since 2005. The mechanisms regulating the dominance and toxicity of P. autumnale are still unclear, as these blooms can reach high biomass in low nutrient conditions. Benthic biofilms are composed of multiple taxa and usually harbor a complex community of bacteria and other microbes, which can change over time and interact to facilitate biofilm development and metabolic processing. Prior to this thesis, the microbial composition of P. autumnale-dominated biofilms was unknown. This study provides insights into the relationships of this neurotoxic cyanobacterium with microbial components of the biofilm community. Benthic biofilms were sampled every two to four days for 32 days from three sites in the Hutt River (Wellington) following a high flow event. A combination of microscopy and molecular techniques (bacterial ARISA and Illumina™ sequencing) were used to identify the micro-algal and bacterial components of the biofilm throughout its development. Variation in total anatoxin production was measured using LC-MS and changes in toxic P. autumnale cell numbers were quantified using QPCR. A suite of environmental variables (point velocity, depth, flow, conductivity, temperature and nutrients) were also monitored throughout the study period. Three distinct phases of microbial succession were identified (early, mid and late) using non-metric multidimensional cluster analyses. The micro-algal community composition (including P. autumnale) shifted from early to mid-phase ca. 16 days after the flushing flow and from mid to late phase at ca. day 30. The ARISA and Illumina™ sequencing showed the bacterial community shifts occurred ca. 4 and 9 days before the respective micro-algal community shifts. These analyses indicate a close coupling of the micro-algal and bacterial communities and may suggest bacterial driven succession. However, bacteria are likely to depend on micro-algal by-products for nutrition from the mid-phases onward and assessment of the metabolic processes occurring within the biofilms is needed to clarify this. Phormidium autumnale was dominant in the biofilm from an early stage in development and grew exponentially despite an influx of diatoms at day 20. None of the environmental parameters measured could explain the temporal variation in micro-algal and bacterial communities, which suggested that intrinsic rather than extrinsic factors were more important in regulating succession. This further supports the hypothesis that biofilm microbes may facilitate P. autumnale dominance. There was a significant variation in anatoxins per cell over time (p = 0.034). Production of anatoxins was greatest in the mid-phase of succession (208 fg cell⁻¹), coinciding with an increase in diatom biomass, which could implicate anatoxins as allelopathic chemicals that alleviate the effects of competition on P. autumnale. Changes in proportions of the different anatoxin variants produced over time also aligned with the three successional phases in both the micro-algal and bacterial communities, providing further evidence of a relationship between anatoxin production and microbial biofilm components. Bacterial taxa of the Alphaproteobacteria were dominant within the early bacterial community, but were surpassed by the Betaproteobacteria and Flavobacteria in mid and late phases. Bacterial genera involved in exopolysaccharide production, alkaline phosphatase activity and biopolymer degradation were identified. These attributes are important in the formation, maintenance and break-down of biofilms and therefore strengthen the likelihood of linkages between the micro-algal and bacterial community. Further investigations into functional roles of the biofilm components are needed to infer relationships between P. autumnale and the bacterial community. A clear pattern of microbial succession is described here and linkages between the micro-algal and bacterial communities are evident. Future work should focus on the functional attributes of microbes occurring at different stages of succession to further understand how P. autumnale dominates these benthic communities.</p>

Characterising the benthic Phormidium autumnale-dominated biofilm community and anatoxin production throughout biofilm succession

<p>There has been an increase in the prevalence and intensity of Phormidium autumnale-dominated benthic blooms in New Zealand over the last decade. This species produces the potent neurotoxins Anatoxin-a, Homoanatoxin-a and their derivatives, and consumption of P. autumnale biofilms has led to over 70 dog deaths since 2005. The mechanisms regulating the dominance and toxicity of P. autumnale are still unclear, as these blooms can reach high biomass in low nutrient conditions. Benthic biofilms are composed of multiple taxa and usually harbor a complex community of bacteria and other microbes, which can change over time and interact to facilitate biofilm development and metabolic processing. Prior to this thesis, the microbial composition of P. autumnale-dominated biofilms was unknown. This study provides insights into the relationships of this neurotoxic cyanobacterium with microbial components of the biofilm community. Benthic biofilms were sampled every two to four days for 32 days from three sites in the Hutt River (Wellington) following a high flow event. A combination of microscopy and molecular techniques (bacterial ARISA and Illumina™ sequencing) were used to identify the micro-algal and bacterial components of the biofilm throughout its development. Variation in total anatoxin production was measured using LC-MS and changes in toxic P. autumnale cell numbers were quantified using QPCR. A suite of environmental variables (point velocity, depth, flow, conductivity, temperature and nutrients) were also monitored throughout the study period. Three distinct phases of microbial succession were identified (early, mid and late) using non-metric multidimensional cluster analyses. The micro-algal community composition (including P. autumnale) shifted from early to mid-phase ca. 16 days after the flushing flow and from mid to late phase at ca. day 30. The ARISA and Illumina™ sequencing showed the bacterial community shifts occurred ca. 4 and 9 days before the respective micro-algal community shifts. These analyses indicate a close coupling of the micro-algal and bacterial communities and may suggest bacterial driven succession. However, bacteria are likely to depend on micro-algal by-products for nutrition from the mid-phases onward and assessment of the metabolic processes occurring within the biofilms is needed to clarify this. Phormidium autumnale was dominant in the biofilm from an early stage in development and grew exponentially despite an influx of diatoms at day 20. None of the environmental parameters measured could explain the temporal variation in micro-algal and bacterial communities, which suggested that intrinsic rather than extrinsic factors were more important in regulating succession. This further supports the hypothesis that biofilm microbes may facilitate P. autumnale dominance. There was a significant variation in anatoxins per cell over time (p = 0.034). Production of anatoxins was greatest in the mid-phase of succession (208 fg cell⁻¹), coinciding with an increase in diatom biomass, which could implicate anatoxins as allelopathic chemicals that alleviate the effects of competition on P. autumnale. Changes in proportions of the different anatoxin variants produced over time also aligned with the three successional phases in both the micro-algal and bacterial communities, providing further evidence of a relationship between anatoxin production and microbial biofilm components. Bacterial taxa of the Alphaproteobacteria were dominant within the early bacterial community, but were surpassed by the Betaproteobacteria and Flavobacteria in mid and late phases. Bacterial genera involved in exopolysaccharide production, alkaline phosphatase activity and biopolymer degradation were identified. These attributes are important in the formation, maintenance and break-down of biofilms and therefore strengthen the likelihood of linkages between the micro-algal and bacterial community. Further investigations into functional roles of the biofilm components are needed to infer relationships between P. autumnale and the bacterial community. A clear pattern of microbial succession is described here and linkages between the micro-algal and bacterial communities are evident. Future work should focus on the functional attributes of microbes occurring at different stages of succession to further understand how P. autumnale dominates these benthic communities.</p>