Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens

The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

Background Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties. Results Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments. Conclusions These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.

Near-chromosome-level genome assembly of the dark septate endophyte Laburnicola rhizohalophila: a model for investigating root-fungus symbiosis

The novel DSE Laburnicola rhizohalophila (Pleosporales, Ascomycota) is frequently found in the halophytic seepweed (Suaeda salsa). In this paper, we report a near-chromosome-level hybrid assembly of this fungus using a combination of short-read Illumina data to polish assemblies generated from long-read Nanopore data. The reference genome for L. rhizohalophila was assembled into 26 scaffolds with a total length of 64.0 Mb and a N50 length of 3.15 Mb. Of them, 17 scaffolds approached the length of intact chromosomes, and 5 had telomeres at one end only. A total of 10,891 gene models were predicted. Intriguingly, 27.5 Mb of repeat sequences that accounted for 42.97% of the genome was identified, and long terminal repeat retrotransposons were the most frequent known transposable elements (TEs), indicating that TE proliferation contributes to its increased genome size. BUSCO analyses using the Fungi_odb10 dataset showed that 95.0% of genes were complete. In addition, 292 carbohydrate active enzymes, 33 secondary metabolite clusters, and 84 putative effectors were identified in silico. The resulting high-quality assembly and genome features are not only an important resource for further research on understanding the mechanism of root-fungi symbiotic interactions, but will also contribute to comparative analyses of genome biology and evolution within Pleosporalean species.

KARAKTERISASI BAKTERI TANAH PERTANIAN ORGANIK DAN TANAH PERTANIAN ANORGANIK DAN UJI ANTAGONIS TERHADAP JAMUR AKAR PUTIH (Rigidoporus microporus)

Research on the Characterization and Antagonist Test of Organic Soil Bacteria and Inorganic Farm Soils Against White Root Fungi (Rigidoporus microporus), was studied at the USU FMIPA Microbiology Laboratory, Medan, in May 2018. The method used was the characterization of agricultural soil bacteria with scatter plates and Yeast media. Extract 1%, obtained 3 soil bacterial isolates namely Sp01, Sp02 and Sp03 and 3 isolates from the inorganic agricultural soils Spa1, Spa2, and Spa3 which were characterized by shape, color, elevation edge and edge of the colony. Sp02 and Sp03 bacteria have greater ability to inhibit the growth of Rigidoporus microporus than Sp01 with inhibition zones of 2.5 and 3.5 mm. Sp a1 bacterium has the highest inhibitory ability of 30 mm against Rigidoporus microporus compared to Spa2 and Spa3. Keywords: Bacteria, Rigidoporus microporus, Faarm soils

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

ABSTRACTBackgroundPlants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of these root-associated microbiotas is not well understood. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the US. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soil types.ResultsOur analysis showed that the secretion of BXs affected community composition of rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of the two genetic backgrounds was weaker than that of the presence or absence of BXs, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three soil types. Instead, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae, and enriched various plant pathogenic fungi in the roots.ConclusionsThese findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different field locations. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.

IMPROVED MOBILE BED BIOFILM REACTORS TO TREAT CELLULOSIC WASTEWATERS

The wastewater treatment sector is a very dynamic field, in continuous development. New technologies are developed, or the existing ones are improved [1]. An efficient biological treatment is based on solid small plastic pieces (biofilm carriers) on which different types of microorganisms attach, develop and grow. This technology is known as Moving Bed Biofilm Reactor (MBBR) technology [2]. The most common materials used for the biofilm carriers’ realization are based on high density polyethylene. This technology is not yet applied for the treatment of the cellulosic wastewaters, since cellulose is hard to be removed by using conventional microorganisms that are usually used in biological wastewater treatment. Some of the authors propose an improved material for carriers to be used in tertiary treatment for textile, paper-mill or tannery wastewaters [3]. The biofilm carriers are adapted for fungal activity. The selected fungal strains (White Root Fungi) capable of removing cellulose from wastewaters [4] will be immobilized on special biofilm carriers. The improved carrier is designed to be used in a MBBR and to favour fungal development in the presence of competing bacteria. Several laboratory experiments related to the fungal attachment on the improved carriers were realized and the results are presented in the paper.

POTENSI JAMUR ENDOFIT TANAMAN KARET DALAM MENGHAMBAT PERTUMBUHAN JAMUR AKAR PUTIH (Rigidoporus microporus) SECARA IN VITRO

One of the environmentally friendly control alternatives that can be done, namely by utilizing biological agents in the form of endophytic fungi that are antagonistic. This study aims to study and obtain information about the potential of endophytic fungi in inhibiting white root fungi in vitro. Endophytic fungi isolation is carried out by sterilizing the surface of the stem of the rubber plant and culture it on agar nutrient media. Five endophytic bacterial isolates were obtained from the roots of rubber plants, respectively: JEB01, JEB02, JEB03, JEB04 and JEB05. Fungal isolates were tested antagonistically in vitro against Rigidoporus microporus. Two fungal isolates, JEB01 and JEB02 showed the best antagonist in inhibiting the growth of pathogenic fungi Rigidoporus microporus in vitro. Keywords: endophytic fungi, in vitro, Rigidoporus microporus, rubber plants (Hevea brasilliensis