by Ylenia Vimercati
Mount Kilimanjaro, the tallest free-standing mountain on Earth located on the Kenya-Tanzania border, is well known for its collapsed summit forming the Reusch crater, and its permanent plateau glaciers. But, is this “island of the cryosphere” going to last long? In recent years Mt. Kilimanjaro has become an “icon” of climate change due to its dramatic ice loss that has attracted much attention among scientists, especially microbiologists, who are concerned about the fate of biological communities surviving in this harsh environment. Mt. Kilimanjaro seems to be of interest to astrobiologists too for its extreme environmental conditions considered as potential analogues for habitable zones on Mars.
85% of the ice cover has already disappeared and an increase of incoming radiation and a severe drop in atmospheric moisture are posing a threat to Mt. Kilimanjaro glaciers and their unique microbial community that may be lost forever along with the stored information on climatic and environmental changes through time. Up to now there have been no investigations published on the high-elevation microbial diversity of the habitats at the top of Mt. Kilimanjaro and on how these communities are responding to climate change drivers. This makes it extremely important and urgent to study the microbiology of the glaciers at the top of the mountain.
A cutting-edge study published in July in Scientific Reports led by the AMO’s Lara Vimercati describes the diversity of soil and ice-dwelling microbes near the summit of Mt. Kilimanjaro. Field collections took place in 2012 at the border of the tabular-shaped plateau glacier in the Southern Icefield at 5772 m elevation. Surprisingly, ice and periglacial soils contain rich and diverse assemblages of Bacteria and Eukarya, probably indicating high rates of dispersal to the top of the mountain and/or that the habitat is more conducive to microbial life than previously expected. As for Bacteria, richness was high for both soil and ice communities and the high diversity encountered in the samples can be explained by glaciers supporting active microbes that gain nutrients from the atmosphere. According to the study, aeolian transportation seems crucial in the assembly of bacterial communities on Mt. Kilimanjaro.
Results from the community composition analysis revealed that bacteria from soil and ice were dominated by Betaproteobacteria, especially members of the Comamonadaceae family. Scientists classified bacterial taxa into “endemic” (meaning only found on Mt. Kilimanjaro) and “non-endemic” (meaning also found elsewhere) and found that most bacterial communities within the second category were cosmopolitan. Within the Bacteria the dominant Polaromonas clade was selected to test its biogeographical distribution and analysis revealed that spatial structuring was not evident, supporting the contention that Polaromonas phylotypes are globally distributed within all glacial habitats. According to the study these Betaproteobacteria may use multiple aeolian deposited carbon sources making wind transportation fundamental for the assembly of bacterial communities. It is still unclear whether Polaromonas are indigenous to ice or they are transients from the upper atmosphere; they may be being constantly deposited in glacial systems, but not necessarily growing there.
As for Eukarya, phylogenetic analysis showed that ice communities were dominated by Cercozoa, while in soil they were the most abundant taxonomic group together with Chlorophyta. Within the Cercozoa, the authors observed that most sequences fell within the Trinematidae and the Vampirellida orders. Sequencing analysis of Vampirellida revealed that they are different from any other taxa in Genbank suggesting that this is a unique Vampirellida community with a high endemicity on Mt. Kilimanjaro probably associated with the fumarolic activity of the summit. Observations showed that they were more abundant in ice samples compared to soil samples indicating that the Vampirellida may have come from the ice. Testate amoebae abundance within the Cercozoa was high and it is probably sustained by feeding on fungi, algae and bacteria.
This study is a first step towards gaining information on the global dispersal of microbes at high elevation sites in Africa. Despite the isolation of Mt. Kilimanjaro from any other mountain, the summit represents an oasis where microbes in the upper atmosphere thrive. Microbes can disperse over long distances, but they require specific adaptations to survive in high-elevation icy environments. The authors state that more work is needed to determine if these organisms can actually grow on Mt. Kilimanjaro or if they are just transient wind-dispersed microorganisms. Microbial diversity was higher than expected compared to other high volcanoes in drier regions. Bacterial community richness and diversity was quite high, and the presence of cosmopolitan bacteria suggests that the effect of distance is overwhelmed by continuous aeolian dispersal.
As Mt. Kilimanjaro’s icecaps continue to vanish undisturbed, understanding the biodiversity and function of the organisms that live in the glacial and periglacial soils of the summit is extremely important and requires our attention. These ecosystems may soon disappear along with its biodiversity and pool of genes adapted to these extreme environments. The study of these life forms may also provide us a model for viable habitats for life on Mars where similar conditions may have existed or still exist.
Vimercati L, Darcy JL, Schmidt SK (2019) The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Scientific Reports 9:10676
by Cliff Bueno de Mesquita and Lara Vimercati
Dothideomycetes is the largest and most diverse class of fungi in the phylum Ascomycota, with 19,000 species currently described. Species within the Dothideomycetes class range from plant pathogens, to saprotrophs to some that exist as the fungal partner in the lichen symbiosis to others that live on rocks. Interestingly, we have found Dothideomycetes in some of the most extreme environments on Earth. A taxon from the Dothideomycetes class was one of the taxa that responded to our water and water + nutrient experiment in hyper-arid soils collected from ~5000 meters elevation on Volcán Llullaillaco in the Atacama Desert in Chile. In this experiment, soils in Petri dishes placed in a freeze-thaw chamber were given water or water + nutrients on three separate occasions.
Figure 1. Dothideomycetes cultures and microscopy photos. a–c Rachicladosporium monterosium. a Colony appearance. b–c Hyphae septate, subhyaline to pale brown. d–g Rachicladosporium paucitum d Colony appearance. e–g Meristematic development of hypae, pale brown. h–j Rachicladosporium inconspicuum. From Egidi et al. 2013
Fungi within the Dothideomycete class significantly increased with multiple water additions in soil microcosms that were amended with organic carbon and nutrients. Dothideomycetes are known to be highly resistant to a number of extreme environmental conditions by developing avoidance strategies (Selbmann et al. 2015). For example, they can tolerate oligotrophy, repeated freeze-thaw stress (Onofri et al. 2007, 2008), radiation and dehydration (Onofri et al. 2012) by producing extracellular polymeric substances (EPS), melanin and compatible solutes. Many genera can form deeply melanized meristematic colonies and produce extracellular polysaccharides to ameliorate UV and osmotic stresses (Selbmann et al. 2005). Their unique colony morphology helps minimize exposure to external stressors by decreasing their surface to volume ratio and appear to have optimized a slow but persistent growth strategy for extremely cold and barren habitats (Ruibal et al. 2009). They are characterized by simple life cycles that can be completed during short periods of time when favorable conditions prevail (Selbmann et al. 2015). Oligotrophy of the extreme environments where they are found and the high metabolic costs to synthetize compounds related to stress resistance account for their slow growth velocity (Selbmann et al. 2014) and help explaining why the relative abundance of this taxon increases significantly only after the second and third water additions to the +WN treatments in this experiment, but not the initial additions.
Egidi, E., de Hoog, G.S., Isola, D., Onofri, S., Quaedvlieg, W., Vries, M.D., Verkley, G.J., Stielow, J.B., Zucconi, L., & Selbmann, L. (2013). Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies. Fungal Diversity, 65, 127-165.
Onofri S, Barreca D, Selbmann L, Isola D, Rabbow E, Horneck G, de Vera JPP, Hatton J, Zucconi L (2008) Resistance of Antarctic black fungi and cryptoendolithic communities to simulated space and Mars conditions. Stud Mycol 61:99–109
Onofri S, de la Torre R, de Vera JP, Ott S, Zucconi L, Selbmann L, Scalzi G, Venkateswaran K, Rabbow E, Horneck G (2012) Survival of rock-colonizing organisms after 1.5 years in outer space. Astrobiology 12:508–516
Onofri S, Selbmann L, de Hoog GS, Grube M, Barreca D, Ruisi S, Zucconi L (2007) Evolution and adaptation of fungi at the boundaries of life. Adv Space Res 40:1657–1664
Ruibal C, Gueidan C, Selbmann L, Gorbushina AA, Crous PW, Groenewald JZ, Muggia L, Grube M, Isola D, Schoch CL, Staley JT, Lutzoni F, de Hoog GS (2009) Phylogeny of rock inhabiting fungi related to Dothideomycetes. Stud Mycol 64:123–133
Selbmann L, de Hoog GS, Mazzaglia A, Friedmann EI, Onofri S (2005) Fungi at the edge of life: cryptoendolithic black fungi from Antarctic deserts. Stud Mycol 51:1–32
Selbmann, L., de Hoog, G.S., Zucconi, L., Isola, D. and Onofri, S., 2014. Black yeasts in cold habitats. In Cold-adapted Yeasts (pp. 173-189). Springer, Berlin, Heidelberg.
Selbmann, L., Zucconi, L., Isola, D. and Onofri, S., 2015. Rock black fungi: excellence in the extremes, from the Antarctic to space. Current genetics, 61(3), pp.335-345
by Eli Gendron
The Chrysophyceae or ‘golden algae’ are a class of yellow-brown pigmented algae who get their pale coloration from the pigment fucoxanthin, which masks the darker greens of chlorophyll a + c, and generally have a motile life cycle stage where single cells develop heterokonts (pair of flagella of unequal length and often perform different functions) (Nicholls and Wujek 2003). Chrysophytes are usually found in freshwater ecosystems and associated with oligotrophic (low nutrient) environments resulting in them acting as the base nutrient source for many heterotrophic organisms (Rawson 1956). Due to their preference for oligotrophic freshwater ecosystems, members of Chrysophyceae are often abundant in the low nutrient waters of alpine lakes, streams, and rivers (Ward 1994). In particular, the Chrysophyte Hydrurus foetidusis commonly observed in glacial melt streams and other environments with low nutrients, high light availability, and rapidly moving water (Moog and Janecek 1991). H. foetidusalso shows a preference for cold water temperatures and temperatures above 16˚C are lethal (Klaveness 2017). H. foetidusis a surface attached multicellular alga (Fig.1A) which grows on stream beds and creates fibrous macro-structures (Fig.1B) which act as residence and food for invertebrate and grazing protist communities (Moog and Janecek 1991). In the attached stage of its life cycle, Hydrurusis non-motile, but when it is ready to colonize new locations, it sheds motile single cells (zoospores, Fig.1C) which possess the characteristic heterokont (Hoffman et al.1986). H. foetidus can also be found across a wide geographic range, including both Antarctica and the Arctic. Lastly, due to its wide geographic range, significant preference for oligotrophic environments, sensitivity to temperature, and its key role in nutrient availability in oligotrophic environments, H. foetidus and its relatives make ideal candidates for indicators to monitor changes in ecosystem health, stability, and trophic status under shifts in climatic conditions (Klaveness 2017).
Figure 1. Morphology of Hydrurus foetidus’ structures. Light microscope pictures of the multicellular structure (A), macrostructure (B), and illustration of the single cell zoospore (C) of Hydrurus foetidus. Scale bars are 5 µm (A), 5 mm (B), and 5 µm (C). Note the diagram of the zoospore (C) includes the heterokont flagella. The heterokont are likely an adaptation to aquatic environments as a way to facilitate the spread of offspring in order to establish new macrostructures downstream. Pictures and figures were adapted from Klaveness 2017 (A, B) and Remias et al. 2013 (C).
Hoffman, L.R., Vesk, M., and Pickett-Heaps, J.D. (1986) The cytology and ultrastructure of zoospores of Hydrurus foetidus (Chrysophyceae). Nord. J. Bot. 6: 105–122.
Klaveness, D. (2017) Hydrurus foetidus (Chrysophyceae)—an inland macroalga with potential. J. Appl. Phycol.29: 1485–1491.
Moog, O. and Janecek, B.F.U. (1991) River flow, substrate type, and Hydrurus density as major determinants of macroinvertebrate abundance, composition and distribution. Int. Vereinigung für Theor. und Angew. Limnol. Verhandlungen24: 1888–1896.
Nicholls, K.H. and Wujek, D.E. (2003) Chrysophycean Algae Elsevier Inc.
Rawson, D.S. (1956) Algal Indicators of Trophic Lake Types. Limnol. Oceanogr.1: 18–25.
Ward, J.V. (1994) Ecology of alpine streams. Freshw. Biol.32: 277–294.
by Cliff Bueno de Mesquita
In our recent and ongoing experiments on the effects of herbicides on soil microbes, we found one species of fungus, Mortierella elongata, that was not negatively affected by the herbicide Glyphosate (ingredient in Roundup), and actually responded positively to the surfactant it is usually spread with, Agridex. Soils collected from the nearby Chatfield Farm outside of Denver had received treatments of Glyphosate, Agridex, Promax (another surfactant), Agridex and Glyphosate combined, and controls with no chemical additions.
M. elongata is a fungus in the Mucoromycota phylum. Mortierella species are typically saprotrophs but also grow on the surface of roots. They are capable of degrading complex carbon compounds such as chitin and hemicellulose. They reproduce via formation of thick-walled spores called zygospores, which are produced by many other species of fungi as well as algae (Gams, Chien, and Domsch 2009). Typically, they are not pathogenic.
Figure 1. Morphology of Mortierella elongata CNUFC-YR329-1. A, D colony on potato dextrose agar; B, E colony on oatmeal agar; C, F colony on water agar; (A-C: observed view, D-F: reverse view). G-I young sporangia on sporangiophores; J the collar at the top of the sporangiophore (white arrow). K sporangiosphores (scale bars: G-K ¼ 20 lm). From Nguyen et al. 2019.
M. elongata has been isolated and cultured. It produces Arachidonic acid (an omega-6 fatty acid also found in red meat), as well as Eicosapentaenoic acid (also known as EPA omega-3 fatty acid), both of which people take as supplements (Bajpai, Bajpai, and Ward 1991; Yamada, Shimizu, and Shinmen 1987). However, it appears that there was never large-scale commercial production of M. elongata for those purposes. Another interesting thing about this fungus is it contains a bacterium inside of it, called an endobacterium, which was identified as Mycoavidus cysteinexigens (Ohshima et al. 2016). Researchers suggested that this endobacterium was responsible for the production of nitrous oxide (Sato et al. 2010), a greenhouse gas, and there has been considerable interest in the bacterium, as its whole genome has been sequenced and assembled (Fujimura et al. 2014).
Our result with M. elongata highlights the importance of studying chemicals used to help spread herbicides, in addition to the herbicide itself. Stay tuned in future months for more results from our herbicide experiment!
Bajpai, P., P. K. Bajpai, and O. P. Ward. 1991. “Eicosapentaenoic Acid (EPA) Formation: Comparative Studies with Mortierella Strains and Production by Mortierella Elongata.” Mycological Research 95(11): 1294–98. http://dx.doi.org/10.1016/S0953-7562(09)80577-7.
Fujimura, R. et al. 2014. “Draft Genome Sequence of the Betaproteobacterial Endosymbiont Associated with the Fungus Mortierella Elongata FMR23-6.” Genome Announcements 2(6): 2010–11.
Gams, W., Chiu-Yuan Chien, and K.H. Domsch. 2009. “Zygospore Formation by the Heterothallic Mortierella Elongata and a Related Homothallic Species, M. Epigama Sp.Nov.” Transactions of the British Mycological Society 58(1): 5–13. http://dx.doi.org/10.1016/S0007-1536(72)80065-2.
Nguyễn, Thưởng & Won Park, Se & Pangging, Monmi & Lee, Hyang. (2019). Molecular and Morphological Confirmation of Three Undescribed Species of Mortierella from Korea. Mycobiology. 47. 31-39. 10.1080/12298093.2018.1551854.
Ohshima, Shoko et al. 2016. “Mycoavidus Cysteinexigens Gen. Nov., Sp. Nov., an Endohyphal Bacterium Isolated from a Soil Isolate of the Fungus Mortierella Elongata.” International Journal of Systematic and Evolutionary Microbiology 66(5): 2052–57.
Sato, Yoshinori et al. 2010. “Detection of Betaproteobacteria inside the Mycelium of the Fungus Mortierella Elongata.” Microbes and Environments 25(4): 321–24. http://joi.jlc.jst.go.jp/JST.JSTAGE/jsme2/ME10134?from=CrossRef.
Yamada, Hideaki, Sakayu Shimizu, and Yoshifumi Shinmen. 1987. “Production of Arachidonic Acid by Mortierella 1S-5.” Agricultural and Biological Chemistry 51(3): 5–10.
by Adam Solon
When studying eukaryotic microbes, familiar groupings such as fungi, green algae, and micro animals, such as Tardigrades (water bears!), are usually found in communities. However, there also exists a large diversity of life that do not fit into those taxonomic assignments. Many are members of the broad grouping known as Protists. Protists are not united in any sort of phylogenetic connection and exist as a catchall for eukaryotic microbes that are not fungi, green algae, or animals. Among those are the organisms that make up the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria). The Stramenopiles include a wide range of organisms including kelp, diatoms, and parasites such as the genus Phytophthora, infamous for causing the Great Irish Potato famine (Derelle et al. 2016). When conducting a lab experiment with soils from Antarctica we found large relative abundances of Xanthophyceae, a member of the Stramenopiles group.
Xanthophyceae are a taxonomic class of the Stramenopiles and have the common name yellow-green algae. While they have the name algae, they are distantly related to the more commonly known green algae. Morphological-physiological characteristics that distinguish Xanthophyceae include: photosynthesis (i.e. use sunlight for energy, like plants), heterokonate (i.e. two flagella (threadlike appendages typically used for swimming) of different lengths, one forward tinsel flagellum and one backward whiplash flagellum); and capability of asexual or sexual reproduction (Sahoo & Kumar 2015). They also have a wide variety of characteristics in which they may differ including: uninucleate or multinucleate; unicellular, colonial or filamentous; and various combinations of the following pigments which give them a yellowish-green color- chlorophyll a and c, β-carotene and xanthophylls (Maistro et al. 2017). One of the clear distinctions between yellow-green algae and green algae is a lack of chlorophyll b in yellow-green algae.
Typically found in freshwater and moist soils, with a few in marine habitats, Xanthophyceae have been discovered in both polar regions (Novis et al. 2015, Kvíderová & Elster 2017). Using soils collected from Taylor Valley in the Dry Valleys of Antarctica, we introduced inputs of water along with an initial treatment of nitrogen and phosphorus to the normally dry, oligotrophic (nutrient poor) soils from this polar desert. These little critters were able to take advantage of those nutrient additions and the subsequent water inputs and contributed to the development of a biocrust that formed on the surface. Our DNA-seq analysis revealed they made up a significant level of relative abundance in those crusts (Fig 1).
Derelle, R., López-García, P., Timpano, H., & Moreira, D. (2016). A phylogenomic framework to study the diversity and evolution of stramenopiles (= heterokonts). Molecular biology and evolution, 33(11), 2890-2898.
Kvíderová, J., & Elster, J. (2017). Photosynthetic activity of Arctic Vaucheria (Xanthophyceae) measured in microcosmos. Czech Polar Reports, 7(1), 52-61.
Maistro, S., Broady, P., Andreoli, C., & Negrisolo, E. (2017). Xanthophyceae. Handbook of the Protists, 407-434.
Novis, P. M., Aislabie, J., Turner, S., & McLeod, M. (2015). Chlorophyta, Xanthophyceae and Cyanobacteria in Wright Valley, Antarctica. Antarctic Science, 27(5), 439-454.
Sahoo, D., & Kumar, S. (2015). Xanthophyceae, Euglenophyceae and Dinophyceae. In The algae world (pp. 259-305). Springer, Dordrecht.
by Cliff Bueno de Mesquita
This month I’ll write about another microbe from my litter addition experiment. One of the dominant fungi on/in the leaves of the alpine cushion plant Silene acaulis was Phaeosphaeria silenes-acaulis, which actually gets its name due to its presence on the Silene acaulis plant! Not only was this fungus abundant in Silene leaves, but it was not present in the other two plant species’ leaves that I studied, highlighting it’s specificity to Silene, although it has also been reported in a couple of other arctic/alpine plant species (Steinke and Hyde 1997, Tojo et al. 2013). The community composition of leaf fungi (and bacteria too) was significantly different in the three plant species I studied, and this was partially driven by the abundance of P. silenes-acaulis in Silene acaulis and not the other two species (Figure 1). Statistical analysis showed that P. silenes-acaulis contributed 14% to differences in fungal communities between Silene and the bunchgrass Deschampsia, and 31% to differences in fungal communities between Silene and the edible alpine mountain sorrel plant Oxyria.
The genus Phaeosphaeria is in the phylum Ascomycota and contains saprotrophic fungi that function as decomposers. Sixteen different species in the genus have been previously reported in arctic and alpine ecosystems, including Svalbard, Norway and the Tatra Mountains in Slovakia (Tojo et al. 2013, Kozłowska et al. 2016). These fungi are adapted to these ecosystems by having a simple life cycle, forming thick and deeply pigmented walls, and having ascospores (reproductive spores produced by fungi in the Ascomycota phylum, Figure 2) with gelatinous sheaths (Leuchtmann 1987). Another species of note in the genus is Phaeosphaeria oryza, which associates with rice and is an important biological control agent of rice blast disease (Ohtake et al. 2008).
As with many microbial taxa, we have now done the basic ecological work of sequencing and phylogenetic classification, but information is lacking on function. As I have done with some of my root samples, future work could attempt to isolate this fungus by placing Silene acaulis leaves on petri dishes with agar and an energy source, and then do further experiments to examine the role of the fungus either in decomposition or Silene acaulis plant health.
Bueno de Mesquita C.P., Schmidt S.K., Suding K.N. (2019) Species-specific plant-microbe interactions in an early successional ecosystem. Plant and Soil in review.
Kozłowska M., Mułenko W., Bacigálová K, Wołczańska A., Świderska-Burek U., Pluta M. (2016) Microfungi of the Tatra Mountains. Part 7. Correction of some data from herbaria and the literature. Acta Mycologica 51(2):1081.
Leuchtmann A. (1987) Phaeosphaeria in the Arctic and Alpine Zones. In: Laursen G.A., Ammirati J.F., Redhead S.A. (eds) Arctic and Alpine Mycology II. Environmental Science Research, vol 34. Springer, Boston, MA
Ohtaka N., Kawamata H., Narisawa K. (2008) Suppression of rice blast using freeze-killed mycelia of biocontrol fungal candidate MKP5111B. Journal of General Plant Pathology 74: 101-108
Quaedvlieg W., Verkley G.J., Shin H.D., Barreto R.W., Alfenas A.C., Swart W.J., Groenewald J.Z., Crous P.W. (2013) Sizing up Septoria. Studies in Mycology 75: 307-390.
Tojo M., Masumoto S., Hoshino T. (2013) Phytopathogenic Fungi and Fungal-Like Microbes in Svalbard. In: Imai R., Yoshida M., Matsumoto N. (eds) Plant and Microbe Adaptations to Cold in a Changing World. Springer, New York, NY
Steinke T.D., Hyde K.D. (1997) Phaeosphaeria capensis sp. nov. from Avicennia marina in South Africa. Mycoscience 38: 101-103.
by Cliff Bueno de Mesquita
I have finished analyzing data from an experiment I did looking at how adding plant litter (dead leaves) affects microbial communities in unvegetated soils. Since microbial growth in unvegetated soils can be limited by carbon, and plant leaves contain lots of carbon, we expected to see changes in microbial communities as different microbes increase in growth to decompose the leaves. Besides that, leaves also harbor their own microbial communities, which also get added to soil when they fall. Botrytis caroliniana (Figure 1) is a species of fungus that was abundant in plant litter but also varied among plant species. B. caroliniana was especially abundant in the leaves of the mountain sorrel plant Oxyria digyna and less abundant in the grass Deschampsia cespitosa and the cushion plant Silene acaulis.
Botrytis is a relatively well studied fungal genus with 22 described species, which typically cause disease in plants (Williamson et al. 2007). Botrytis species can be both biotrophs (eating living material) or necrotrophs (eating dead tissues). Several books have been written about the genus, focusing on their negative effects on important crop species (Elad et al. 2007). For example, the species Botrytis cinerea is reported to cause gray mold disease on 200 crop species, including cabbage, lettuce, broccoli, beans, grapes, strawberries, raspberries, and blackberries (Figure 2, Williamson et al. 2007). Botrytis caroliniana gets its name because it was first isolated from blackberry in South Carolina (Li et al. 2012). It has also been reported to cause gray mold disease on strawberries in North Carolina (Fernández-Ortuño et al. 2012). It is closely related to Botrytis fabiopsis and Botrytis galanthina, which cause gray mold disease in broad bean and snowdrop plants (Li et al. 2012).
Clearly, fungi in this genus are pathogens that can have major impacts on wild plants and agricultural crops. The market size for anti-Botrytis products was estimated at $15-25 billion USD (Elad et al. 2007). Now that we know that Botrytis caroliniana is abundant on Oxyria digyna leaves, we can conduct more specific research on the role of this fungus in plant health and plant communities in the alpine.
Elad Y, Williamson B, Tudzynski P, Delen N (eds) (2007) Botrytis: Biology, Pathology and Control. Springer, Dordrecht, The Netherlands
Fernández-Ortuño D, Li XP, Wang F, Schnabel G (2012) First Report of Gray Mold of Strawberry Caused by Botrytis caroliniana in North Carolina. Plant Dis. doi: 10.1094/pdis-12-11-1018-pdn
Li X, Kerrigan J, Chai W, Schnabel G (2012) Botrytis caroliniana , a new species isolated from blackberry in South Carolina. Mycologia 103:650–658. doi: 10.3852/11-218
Williamson B, Tudzynski B, Tudzynski P, Van Kan JAL (2007) Botrytis cinerea: The cause of grey mould disease. Mol Plant Pathol 8:561–580. doi: 10.1111/j.1364-3703.2007.00417.x
by Cliff Bueno de Mesquita
We have started another round of microscopy here in the AMO. We are collaborating with the Suding Lab on understanding how nitrogen deposition and plant species interactions affect microbial communities. One aspect of the work, as in some of our other projects, is to quantify how much of the plant roots contain certain fungi. I have previously written about both arbuscular mycorrhizal fungi and dark septate endophytes, which are two groups of fungi that inhabit plant roots, but there is another – fine root endophytes – that I will tell you about today.
Fine root endophytes (FRE) are a newly classified group of fungi that are characterized by having very fine hyphae. FRE were once considered to be arbuscular mycorrhizal fungi until further genetic work was able to distinguish them. Morphologically, they can be distinguished by their very fine hyphae, which are less the 2 µm wide – that’s 0.002 millimeters. But with the help of the microscope we can view them and identify them as FRE. They look like little fine blue lines (because we stain them with a blue dye) running all throughout the plant roots (Figure 1). Several studies have suggested that FRE can help plants uptake phosphorus, which means they may be functionally similar to arbuscular mycorrhizal fungi. FRE were once thought to be the species Glomus tenue, now reclassified as Planticonsortium tenue, but now several different morphologies have been observed and it is likely that there are several different species of fine root endophytes.
FRE are distributed globally, have been reported in 53 plant families, and have been found in all major habitat types. As we and others continue to quantify the amount of FRE in various plant species and various environments, we can learn more about the ecology of this potentially important fungal group. Additionally, more experiments are needed to learn more about the functioning of FRE.
Orchard S, Hilton S, Bending GD, et al (2017a) Fine endophytes (Glomus tenue) are related to Mucoromycotina, not Glomeromycota. New Phytol 213:481–486. doi: 10.1111/nph.14268
Orchard S, Standish RJ, Dickie IA, et al (2017b) Fine root endophytes under scrutiny: a review of the literature on arbuscule-producing fungi recently suggested to belong to the Mucoromycotina. Mycorrhiza 27:619–638. doi: 10.1007/s00572-017-0782-z
Walker C, Gollotte A, Redecker D (2018) A new genus, Planticonsortium (Mucoromycotina), and new combination (P. tenue), for the fine root endophyte, Glomus tenue (basionym Rhizophagus tenuis). Mycorrhiza 28:213–219. doi: 10.1007/s00572-017-0815-7
By Eli Gendron
Diatoms are a unique life form that can be found in a wide range of environments, from the soils of the arctic and the some of the highest mountains in the world to freshwater lakes across the globe and throughout our oceans (Mann & Droop 1996). One of the characteristics that make diatoms so unique is the glass like shell they build out of silica which often leads them to have regular geometric shaped cells (see Figure 1). These single celled organisms often form colonies that take many forms such as the chains seen in Figure 1. Diatoms are almost always photosynthetic but several strains have been found to be capable of mixotrophy and heterotrophy, meaning they are capable of living off organic matter (Villanova et al. 2017; Tan & Johns 1996).
Figure 1. Image of Fragilaria capucina as seen under a microscope. Left: Image of Fragilaria capucina taken in Chico, Washington, USA; Chico Creek, 400x magnification, DIC – 13 Jul 2008. Right: Image of Fragilaria capucina taken in Bremerton, Washington, USA; Kitsap Lake, 1000x magnification, DIC – 11 Oct 2008. Images curated by http://www.algaebase.org/search/species/detail/?species_id=31451&distro=y#distro
Diatoms such as Fragilaria capucina are a common occurrence in freshwater habitats around the world; however, they tend be low in abundance in oligotrophic (low nutrient) ecosystems. When an ecosystem is exposed to more nutrients than naturally occur, usually through pollution such as nitrogen in fertilizer run off, it becomes eutrophic (abundant nutrients) leading to blooms of previously rare organisms. Fragilaria capucina is one such diatom that is highly resistant to pollution and can often be found thriving in eutrophic conditions (Rott et al. 1998). Armed with this type of knowledge we can monitor communities of easily obtainable species to use as indicators of ecosystem status including catching pollution early.
Mann, D.G. & Droop, S.J.M. (1996) Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336: 19-32
Rott E, Duthie HC, Pipp E. 1998. Monitoring organic pollution and eutrophication in the Grand River, Ontario, by means of diatoms. Can J Fish Aquat Sci 55:1443–1453.
Tan, C.K. and Johns, M.R., 1996. Screening of diatoms for heterotrophic eicosapentaenoic acid production. Journal of Applied Phycology, 8(1), pp.59-64.
Villanova, V., Fortunato, A.E., Singh, D., Dal Bo, D., Conte, M., Obata, T., Jouhet, J., Fernie, A.R., Marechal, E., Falciatore, A. and Pagliardini, J., 2017. Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum. Phil. Trans. R. Soc. B, 372(1728), p.20160404
by Cliff Bueno de Mesquita
Happy new year’s eve from all of us here at the AMO! I am writing this post from little Rhode Island (where I grew up), so I decided to write about a local microbe. So this month’s microbe is a genus called Phytophthera. Phytophthera is a type of microorganism called an oomycete, which is different from, say, a bacterium or a fungus. Oomycetes are often described as being quite similar to fungi, but they form their own unique lineage on the phylogenetic tree of life. They are filamentous, spore-producing organisms that often function as either saprotrophs (organisms that decompose organic matter), or plant pathogens, living on plants and causing them harm. Unlike fungi, whose cell walls are made of chitin, Phytophthera cell walls are made of cellulose. There are 232 described species and species variations in the genus, though it is estimated that there could be as many as 200-300 more that we have not discovered yet!
One of the most common tree diseases in Rhode Island is Phytophthera root rot, which occurs on beech trees. The Phytophthera oomycete in this case infests the beech tree roots, but infected trees will also show bleeding cankers on the trunks (Figure 1). Phytophthera root rot is a leading cause of death for older beech trees. But the Phytophthera genus is actually quite widespread and infects thousands of plant species, including important forest trees like chesnuts, oaks, and alders, and important crops such as strawberries, citrus trees, cucumbers, squash, soybeans, tomatoes and potatoes. Most notably, the species Phytophthera infestans caused the potato blight that led to the Great Irish Potato Famine of 1845-1849!
Goheen EM, Frankel SJ, eds. 2007. Phytophthoras in Forests and Natural Ecosystems. Albany, CA, USA: USDA Forest Service: General Technical Report PSW-GTR-221, 101–15. https://www.fs.fed.us/psw/publications/documents/psw_gtr221/psw_gtr221.pdf
Kaiser Tree Preservation Co. 2018. Top 10 Tree Diseases in Rhode Island. http://kaisertree.com/services/plant-health-care-2-2/top-10-tree-diseases-in-rhode-island/
NCBI. 2018. Phytopthera. NCBI taxonomy. Bethesda, MD: National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=4783&lvl=3&keep=1&srchmode=1&unlock
Nowicki M, Foolad MR, Nowakowska M, Kozik EU. 2011. Potato and tomato late blight caused by Phytophthora infestans: An overview of pathology and resistance breeding. Plant Disease, 96: 4–17, doi:10.1094/PDIS-05-11-0458
Various lab members contribute to the MoM Blog