Brett E. Arenz

Streptomyces competition and co-evolution in relation to plant disease suppression

High densities of antagonistic Streptomyces are associated with plant disease suppression in many soils. Here we review use of inoculation and organic matter amendments for enriching antagonistic Streptomyces populations to reduce plant disease and note that effective and consistent disease suppression in response to management has been elusive. We argue that shifting the focus of research from short-term disease suppression to the population ecology and evolutionary biology of antagonistic Streptomyces in soil will enhance prospects for effective management. A framework is presented for considering the impacts of short- and long-term management on competitive and coevolutionary dynamics among Streptomyces populations in relation to disease suppression.

Screening fungi isolated from historic Discovery Hut on Ross Island, Antarctica for cellulose degradation

Abstract To survive in Antarctica, early explorers of Antarcticas Heroic Age erected wooden buildings and brought in large quantities of supplies. The introduction of wood and other organic materials may have provided new nutrient sources for fungi that were indigenous to Antarctica or were brought in with the materials. From 30 samples taken from Discovery Hut, 156 filamentous fungi were isolated on selective media. Of these, 108 were screened for hydrolytic activity on carboxymethyl cellulose, of which 29 demonstrated activities. Endo-1, 4-β-glucanase activity was confirmed in the extracellular supernatant from seven isolates when grown at 4°C, and also when they were grown at 15°C. Cladosporium oxysporum and Geomyces sp. were shown to grow on a variety of synthetic cellulose substrates and to use cellulose as a nutrient source at temperate and cold temperatures. The research findings from the present study demonstrate that Antarctic filamentous fungi isolated from a variety of substrates (wood, straw, and food stuffs) are capable of cellulose degradation and can grow well at low temperatures.

Introduced and indigenous fungi of the Ross Island historic huts and pristine areas of Antarctica

This review summarizes research concerning Antarctic fungi at the century-old historic huts of the Heroic Period of exploration in the Ross Dependency 1898–1917 and fungi in pristine terrestrial locations. The motivation of the research was initially to identify potential fungal causes of degradation of the historic huts and artifacts. The research was extended to study fungal presence at pristine sites for comparison purposes and to consider the role of fungi in the respective ecosystems. We employed classical microbiology for isolation of viable organisms, and culture-independent DNA analyses. The research provided baseline data on microbial biodiversity. Principal findings were that there is significant overlap of the yeasts and filamentous fungi isolated from the historic sites, soil, and historic-introduced materials (i.e., wood, foodstuffs) and isolated from environmental samples in pristine locations. Aerial spore monitoring confirmed that winter spore counts were high and, in some cases, similar to those found in summer. Microbial diversity varied between the three Ross Island historic sites, and one historic site showed noticeably higher diversity, which led to the conclusion that this is a variable that should not be generalized. Cultured fungi were cold active, and the broader scientific significance of this finding was that climate change (warming) may not adversely affect these fungal species unless they were out-competed by new arrivals or unfavorable changes in ecosystem domination occur.

Cryptococcus vaughanmartiniae sp. nov. and Cryptococcus onofrii sp. nov.: two new species isolated from worldwide cold environments

Twenty yeast strains, representing a selection from a wider group of more than 60 isolates were isolated from cold environments worldwide (Antarctica, Iceland, Russia, USA, Italian and French Alps, Apennines). The strains were grouped based on their common morphological and physiological characteristics. A phylogeny based on D1/D2 ribosomal DNA sequences placed them in an intermediate position between Cryptococcus saitoi and Cryptococcus friedmannii; the ITS1 and ITS2 rDNA phylogeny demonstrated that these strains belong to two related but hitherto unknown species within the order Filobasidiales, albidus clade. These two novel species are described with the names Cryptococcusvaughanmartiniae (type strain DBVPG 4736T) and Cryptococcusonofrii (type strain DBVPG 5303T).

Fungal Diversity in Antarctic Soils

Fungi have contributed to Antarctic ecosystems for >200 million years as, from the fossil record, it has been shown that fungi were present in Antarctica since at least the Triassic Period. Fungi have been reported from a wide variety of soils and substrates in far-ranging geographical locations and diverse habitats in Antarctica; the first reports being from as early as the beginning of the twentieth century. In Antarctic studies, non-lichenized fungi have generally been considered separately from lichenized forms and the list of non-lichenized fungi reported from Antarctic regions (including the sub-Antarctic) is extensive at +1,000 species. Fungi are notorious contaminants especially around sites of human activity, and it is crucial to acknowledge the difficulty of discerning transient/introduced versus indigenous and endemic fungi, and to understand their respective contributions to terrestrial biodiversity. To identify fungi, rigorous decontamination procedures on substrates are used along with conventional culturing methodologies and molecular technologies. This chapter focuses mainly on studies concerning terrestrial non-lichenized fungi published since 1993 and highlights specific taxonomic groups that are most important to Antarctic soil ecosystems.

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities

A blocking primer set based on the technique described by Vestheim and Jarman (2008) was developed to reduce amplification of non-target plant DNA when conducting metagenomic studies on bacterial endophyte communities. Bacterial amplification efficiency was increased 300-fold compared to standard PCR in an Illumina-based study of Sorghastrum nutans leaves.

Rapid and PCR-free DNA Detection by Nanoaggregation-Enhanced Chemiluminescence

The aggregation of gold nanoparticles (AuNPs) is known to induce an enhancement of localized surface plasmon resonance due to the coupling of plasmonic fields of adjacent nanoparticles. Here we show that AuNPs aggregation also causes a significant enhancement of chemiluminescence in the presence of luminophores. The phenomenon is used to introduce a rapid and sensitive DNA detection method that does not require amplification. DNA probes conjugated to AuNPs were used to detect a DNA target sequence specific to the fungus Ceratocystis fagacearum, causal agent of oak wilt. The hybridization of the DNA target with the DNA probes results in instantaneous aggregation of AuNPs into nanoballs, leading to a significant enhancement of luminol chemiluminescence. The enhancement reveals a linear correlation (R2 = 0.98) to the target DNA concentration, with a limit of detection down to 260 fM (260 × 10−15 M), two orders of magnitude higher than the performance obtained with plasmonic colorimetry and absorption spectrometry of single gold nanoparticles. Furthermore, the detection can be performed within 22 min using only a portable luminometer.