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Brown root rot disease (BRRD), caused by

Taxonomic studies including morphological observations and phylogenetic analyses were conducted on Japanese “uragin-take”, an unidentified species from Amazonia, Brazil and their allies. Phylogenetic analyses using ITS, nrLSU and RPB2 regions revealed that “uragin-take”, Neofomitella polyzonata and the unidentified species formed a monophyletic clade separate from the clade including the other four Neofomitella spp. and that “uragin-take” is conspecific with N. polyzonata. Morphological investigations on authentic specimens revealed that Polyporus subradiatus is a prior name for N. polyzonata. We propose Hirticrusta gen. nov. typified by H. subradiata segregated from Neofomitella, and we erected H. amazonica sp. nov. for the unidentified species. Hirticrusta is characterized by annual to biennial and sessile basidiocarps, semicircular to dimidiate pileus, velutinous to tomentose hairs on pileus surface, buff to brown context with a crustose layer indicated by a dark brown line forming a longitudinal section below the superficial hairs, a trimitic hyphal system, crustose layer composed of parallel and densely arranged brown hyphae and cylindrical basidiospores. The new species, H. amazonica is distinguishable from other polypores by downy and long tomentum on the pileus surface (up to 20 mm thick), brown context with a dark brown layer below the tomentum and round pores (5–7/mm).

Ganoderma bambusicola sp. nov. is described and illustrated from tropical Taiwan; it is also found in Laos and Myamar. The species is recognized as new based on morphological study and phylogenetic analyses using three gene regions: ITS, rpb2 and tef1-α. Ganoderma bambusicola has been incorrectly identified as G. neojaponicum in Taiwan for several decades on account of it having a similar shiny dark reddish brown to purplish black pileus surface and a blackish long stipe, but it differs from the latter species in having a homogeneous pileal context. Ganoderma bambusicola is, to date, only known from southern Asia and grows on bamboo roots, while G. neojaponicum occurs on roots or trunks of conifers in Japan, China and Korea. These two species do not have a close relationship according to the present phylogenetic study.

Phellinus noxius, the cause of brown root-rot disease, is an invasive fungal pathogen that causes a white rot among woody plants in Asia, Oceania, and Africa. Because the origin and diversity of this pathogen are unknown, it is difficult to predict its behavior and invasive capacity, especially under future climate-change scenarios. We characterized genetic relationships and ecological differences among P. noxius lineages across eastern Asia and Oceania to better understand evolutionary responses of the pathogen to environmental changes. Sequences of four loci (nuclear large subunit, internal transcribed spacers, partial RNA polymerase II, and partial translation elongation factor – 1 alpha) from 95 P. noxius isolates were used for genetic analyses. Our analyses revealed three genetically distinct lineages of P. noxius: 1) eastern Asia (Japan, Taiwan, Hong Kong, and Malaysia); 2) western Oceania/Japan/Taiwan (including Australia, Palau, Guam, Saipan, Yap, Pohnpei, and Kosrae) with some isolates from Japan and Taiwan; and 3) a distinct group from American Samoa. Population genetic analyses highlighted admixture and migration among the three lineages. Climate-based, species distribution models were used to predict ecological patterns of P. noxius for two genetic lineages: eastern Asia and western Oceania/Japan/Taiwan. Contemporary bioclimatic models depicted potential areas at high risk for P. noxius invasion, and predicted that suitable climate space (potential distribution) is lineage specific. Trade of important economic crops worldwide coupled with changing climates could exacerbate the spread of P. noxius into new geographic areas with suitable habitats for brown root-rot disease.

Two morphologically similar fungi, Fomitiporia torreyae and Fomitiporia punctata, are causal fungi of various tree diseases in Japan and are speculated to be distributed in different climatic zones. Clarifying their distribution ranges and climatic preferences would contribute to the prediction of disease occurrences and consideration of controls. In this study, we predicted the present geographical distributions of F. torreyae and F. punctata in Japan using a Maxent species distribution model to analyze our data and previously published collection records. In addition, we examined the importance of temperature on these predictions via jackknife analysis and evaluated the effects of temperature on mycelial growth and survival to elucidate determinants of their distribution. The predicted potential distributions showed that F. torreyae is mainly distributed in warmer areas compared to F. punctata. Jackknife analysis indicated the high importance of temperature variables for each fungal prediction. The two fungi were usually found at locations within upper or lower temperature limits for the growth and survival of each species. These results suggest that temperature is a key determinant of their distributions in Japan. This is the first report to predict fungal distribution based on species distribution modeling and evaluation of fungal physiological characteristics. This study indicates that the projected global warming will influence the future ranges of the two fungal species.

Melanoderma boninense is described and illustrated as a new species from the Bonin Islands, Japan, on the basis of morphological and phylogenetic investigations. This species is characterized by sessile basidiocarps with an ungulate pileus, a black crust on the pileus surface, pores 4–6/mm, a dimitic hyphal system comprising clamped generative hyphae and cyanophilous skeletal binding hyphae with or without a dextrinoid reaction, cylindrical basidiospores measuring 5.5–7.5 × 2–3 μm, and cystidioles on the sides of tubes and near the pore surface. Morphological examination of authentic specimens of other Melanoderma species revealed that the genus is variable in terms of the shape and size of cystidioles. A black crust on the pileus surface composed of palisade and highly agglutinated hyphae is a distinctive diagnostic morphological feature of Melanoderma that differentiates it from allied genera. Melanoderma boninense, which is currently known from a restricted area of the Bonin Islands, is potentially threatened by environmental reduction of the type locality due to the invasive tree Bischofia javanica.

Gloeoporus Mont. is characterized by an easily separated gelatinous hymenophore and a continuous hymenium over the pore mouth. Recent molecular taxonomic and phylogenetic research showed that morphological grouping of Gloeoporus is polyphyletic. The lack of comprehensive phylogenetic studies of Gloeoporus exacerbates confusion in determining the taxonomic position of the genus. To delimit the genus Gloeoporus, we performed multi-locus phylogenetic analysis using the internal transcribed spacer (ITS) region, the nuclear large subunit ribosomal DNA (LSU), and the second-largest subunit of RNA polymerase II (rpb2). The phylogenetic analyses revealed that current delimitation of Gloeoporus is not monophyletic. Gloeoporus s.s. includes mostly clamped species lacking cystidia. Some species of Gloeoporus featuring simple septa and cystidia are proposed to be renamed to Meruliopsis. Two new species of Gloeoporus were also observed and they are named Gloeoporus africanus and Gloeoporus orientalis. Fil: Jung, Paul Eunil. Universidad Nacional de Seul; Corea del Sur Fil: Lee, Hyun. Universidad Nacional de Seul; Corea del Sur Fil: Wu, Sheng-Hua. National Museum Of Natural Science; China Fil: Hattori, Tsutomu. Forest Research And Management Organization; Japón Fil: Tomšovský, Michal. Mendel University; República Checa Fil: Rajchenberg, Mario. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina Fil: Zhou, Meng. Beijing Forestry University; China Fil: Lim, Young Woon. Universidad Nacional de Seul; Corea del Sur

The traditional medicinal fungus, Lingzhi, has long been considered to be Ganoderma lucidum, but was recently described as G. lingzhi based on both morphological and molecular data. Months earlier than this description, the species was identified as G. sichuanense by another research group. A sequenced epitype for G. sichuanense was selected that, if accepted, meant that it became a synonym of, and an earlier name for, G. lingzhi. However, the holotype of G. sichuanense is well developed with distinct morphological characters, and its ITS sequence, the DNA barcode for fungal taxonomy, is available. The holotype of G. sichuanense does not possess the typical morphological characteristics of Lingzhi, and the designated epitype is not conspecific with the holotype from morphological, phylogenetic and ecological perspectives. Consequently, the designation of the epitype is considered to conflict with the regulations of the Code and should be rejected. As no other previously published species name matches Lingzhi, the correct name for this fungus is G. lingzhi.

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P. noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single-nucleotide-polymorphisms (SNPs) with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.

The present study elucidated the length structure and habitat segregation of North Pacific spiny dogfish (SPD) Squalus suckleyi in the Tsugaru Strait of northern Japan. Length–frequency distributions using kernel density estimation were determined for SPD captured by the bottom longline fishery landed at Minmaya from 1999 to 2011 and at Ohma from 2007 to 2011. Length–frequency distributions significantly differed between landings at the two ports; SPD at Minmaya were on average larger (65–85 cm precaudal length: PCL) than at Ohma (55–75 cm PCL). This difference is evidence of the length-based spatial segregation of the SPD. The seasonal landing pattern of the SPD was also different between the two ports. The SPD landed at Minmaya were largest during February–June and SPD

The North Pacific spiny dogfish (SPD), Squalus suckleyi, is a commercially exploited shark species that plays an important role in the ecosystem. To elucidate the distribution of the SPD in the North Pacific and to evaluate the effects of sea surface temperature (SST) and prey availability on its distribution, we estimated the probability of SPD presence using a generalized additive model with a binomial error distribution from SPD presence/absence data on 14,824 operations in fishery-independent gillnet surveys between 1972 and 2011. The habitat model was structured in the east and west to reflect differences in the North Pacific oceanic environments. In the east, a higher probability of SPD presence was identified along the coast from the eastern Gulf of Alaska to Queen Charlotte Sound. In the west, it was identified around northern Japan. The estimated distribution was continuous between the two areas, whereas the probability of SPD presence was relatively low. Although the probability of SPD presence was higher at SSTs between 6°C and 12°C, the SST at the peak probability of SPD presence differed between the west and east. The prey species, Japanese sardine, Sardinops melanostictus, and walleye pollock, Gadus chalcogrammus, in the west and boreal clubhook squid, Onychoteuthis borealijaponica, in the east significantly affected the probability of SPD presence, which was higher if the prey species co-existed with SPD. Therefore, SPD might adapt their distribution to that of available prey species. SPD stock assessment and management in these two important areas are required for its sustainable utilization.

The population of Pacific cod inhabiting off northeastern Honshu Japan has remarkably increased in the 3 yr after the Great East Japan Earthquake in 2011. We examined the processes and factors leading to this increase based on the results of estimations of commercial catch and fishing activities, and trawl surveys. Pacific cod was highly exploited from 1 yr old before 2011. However, fishing pressure has markedly decreased after 2011 in the area around Fukushima waters. Fish abundance in 2013 and 2014 was estimated to be more than four-fold of the maximum amount before 2011. The cohort structure of the population in 2013 and 2014 was primarily composed of 2–4-yr-old fish (2010–2011 yr classes) whereas the population in pre-2011 was primarily of 1-yr-old fish. The 2010–2011 yr classes had almost the same population sizes until 1.3 yr old to the pre-2009 yr classes, but became much higher more than 2.8 yr old. Pacific cod from 1.3 to 2.8 yr old were concentrated in the area off Fukushima Prefecture. These results suggest that Pacific cod increased post-2011 not because of the occurrence of strong year classes followed by good recruitments but because of the lower mortality after recruitment owing to reduced fishing mortality. Waters off Fukushima, the primary nursery of Pacific cod, are effectively serving as a marine protected area after the tsunami events. A close coincidence between the nursery area of young fish and the protected area strongly altered the age composition of the population and enhanced fish abundance.

Biogeography of polypores distributed in the Malesian region is reviewed. Some of the species reported from this region are pantropical or paleotropical and widely distributed along the equator. Several species are restricted to lowland areas of Malesia and adjacent regions, and can be classified as Asian or Asian-Oceanian tropical species. Some species have only been recorded from lowland areas of Malesia at present, but detailed distributions are unclear for many of them. Some lowland Malesian species are also distributed in temperate areas of East Asia; among them, few species are circumglobal in the Northern Hemisphere, whereas many others are tropical species showing continuous distributions up to the warm temperate areas of East Asia. Species recorded from highland areas of Malesia include tropical species common to lowland Malesia, temperate species common to temperate Asia, and endemic species in highland areas of Malesia and adjacent regions. Regarding the factors that delimitate distribution of the Malesian polypores, I discuss polypore host preference, response to physical environmental factors, and dispersal ability. Systematics and ecological characteristics are briefly discussed for selected Malesian polypores: Corneroporus subcitrinus, Paratrichaptum accuratum, Postia stellifera and Roseofavolus eos.

To describe a multi-center preliminary experience of treating prosthetic above knee femoropopliteal (AKFP) bypass occlusion by placing a Viabahn stent graft inside the occluded prosthetic bypass graft. Retrospective analysis of consecutive 14 patients (mean age 73.2 ± 10.2, 78.6% male) receiving Viabahn stent graft inside the occluded prosthetic bypass graft for the treatment of prosthetic AKFP bypass occlusion in the collaborating hospitals from November 2016 to June 2019 was performed. Technical success was achieved in all patients. Mean lesion length was 34.0 ± 3.5 cm, concomitant thrombectomy or thrombus aspiration was performed in 11 patients (78.6%), and average of 1.57 ± 0.65 Viabahn stent grafts were used. Mean ankle–brachial index improved from 0.24 ± 0.23 to 0.98 ± 0.14 after the treatment. All patients had preoperative ischemic symptoms with 9 patients (64.3%) having Rutherford class > 4 symptoms; however, all preoperative symptoms resolved after the treatment. During the mean follow-up of 450.9 ± 234.7 days, there were two target lesion revascularizations, leading to a primary patency rate of 92.9% and a secondary patency of 100.0% at 1 year. Placing a Viabahn stent graft inside the occluded prosthetic bypass graft for the treatment of prosthetic AKFP bypass occlusion appears to be effective from our preliminary experience. Even though sample size is limited in our study, it may be considered as a potential treatment option before surgical reintervention.

An archaeological waterlogged polypore was found in the Final Jomon period (circa 2600 years ago) at the Neolithic site of Kitashirakawa in Kyoto, Japan. The fragile polypore was treated with the feather-keratin method that we developed for the preservation of wet organic archaeological materials. The method reinforced the polypore against the collapse caused by air-drying. The anatomical features of the polypore were observed under light microscopy and the host wood present at the edge of the basidiocarp was identified as Morus sp. on the basis of anatomical observations. Eventually, the polypore was identified as Inonotus sanghuang . Macroscopic and microscopic observations were carried out in order to evaluate the effectiveness of the keratin treatment on the polypore tissue. The keratin consolidated to the hyphal cell walls, where it stabilized the thick walled fungal mycelium that makes up the polypore fruiting body.

Trunk rot, caused by Fomitiporia torreyae, is one of the most economically important sap rot diseases on Cryptomeria japonica, especially on a cutting cultivar ‘Sanbu-sugi’. This disease had been reported only from Chiba and Ibaraki prefectures in Japan; however, a similar trunk rot on Japanese cedars was found recently in Kyoto prefecture. We identified the causal agent of the trunk rot on Japanese cedars in Kyoto prefecture, clarified the genotype of ‘Sanbu-sugi’ (sensu stricto) using microsatellite markers, and then investigated the relatedness of these infected cedars with ‘Sanbu-sugi’. The pathogen was identified as F. torreyae by its DNA sequences and morphological characteristics of the fruiting body. The 25 ramets of ‘Sanbu-sugi’ had only one genotype based on eight microsatellite loci. Infected Japanese cedars in Kyoto were comprised of different genotypes and showed no close relatedness to ‘Sanbu-sugi’. This is the first report of trunk rot caused by F. torreyae on cultivars of Japanese ...

Dead wood is an important habitat for forest organisms, and wood decay fungi are the principal agents determining the dead wood properties that influence the communities of organisms inhabiting dead wood. In this study, we investigated the effects of wood decomposer fungi on the communities of myxomycetes and bryophytes inhabiting decayed logs. On 196 pine logs, 72 species of fungi, 34 species and seven varieties of myxomycetes, and 16 species of bryophytes were identified. Although white rot was the dominant decay type in sapwood and heartwood, brown and soft rots were also prevalent, particularly in sapwood. Moreover, white rot and soft rot were positively and brown rot negatively correlated with wood pH. Ordination analyses clearly showed a succession of cryptogam species during log decomposition and showed significant correlations of communities with the pH, water content, and decay type of wood. These analyses indicate that fungal wood decomposer activities strongly influence the cryptogam communities on dead wood.

We describe three new species of Fulvifomes from Thailand, all of which grow on Xylocarpus granatum, a major mangrove tree species in southeastern Asia. Fulvifomes xylocarpicola sp. nov. is characterized by the perennial and sessile basidiocarps, woody context without a distinct crust, pores 4–6/mm, a dimitic hyphal system both in the context and trama, broadly ellipsoid basidiospores measuring 4–5.5 × 3.5–4.5 μm, and occurrence on the stem of X. granatum. Fulvifomes siamensis sp. nov. is characterized by the perennial and sessile basidiocarps, woody context without a crust, pores 7–8/mm, a monomitic hyphal system in the context, subglobose basidiospores measuring 4.5–6 × 4–5 μm, and occurrence on the root or butt of X. granatum. Fulvifomes halophilus sp. nov. is characterized by perennial, sessile basidiocarps, leathery to corky context with a crust near the pileus surface, pores 5–8/mm, a subdimitic hyphal system in the context, subglobose basidiospores measuring 4–5.5 × 3.5–5 μm, and occurrence on the root or butt of X. granatum. Fulvifomes mangrovicus comb. nov. is proposed for Fomes mangrovicus. A key to the worldwide species of Fulvifomes is provided.

Improvement cutting, which decreases tree density by cutting and thinning while leaving logging residues, has been practiced on Okinawa Island since the 1970s and changes not only the vegetation composition but also the amount and composition of woody debris on the forest floor. To quantitatively compare the effect of improvement cutting with the effects of woody debris and vegetation on the community structure of aphyllophoraceous fungi, we conducted a field survey of vegetation composition, the amount and composition of woody debris, and the aphyllophoraceous fungi flora on Okinawa Island in December 2006. We established 3 plots in forest stands without logging and 13 plots in a forest that had undergone improvement cutting from 1 to 22 years before our field survey. The number and volume of woody debris tended to be highest soon after improvement cutting. We recorded 1,172 fungal samples belonging to 81 species in four orders. Fungal species richness was correlated with the composition of the woody debris. Fungal species composition in forest plots 1 year after improvement cutting differed from most of the other logged forests. Variation partitioning revealed that the effects of improvement cutting explained 14.1 % of the total variation in fungal species composition, and that differences in woody debris and vegetation not related to improvement cutting explained 40.4 %. Changes in the composition of woody debris caused by improvement cutting explained at most 2.7 % of the variation. This suggests that improvement cutting does not have a strong effect on fungal community structure, but woody debris does.

Agromonas oligotrophica ( Bradyrhizobium oligotrophicum ) S58 T is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica , in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development ( ndv ) and symbiotic nitrogen fixation ( nif and fix ) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica , with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica . Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC - and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica .

We present a taxonomic study of ‘group Favolus’ and related species in Polyporus. Phylogenetic analyses of nurLSU and ITS regions revealed that the infrageneric ‘group Favolus’ is divided into two main clades. Fungi within the group share laterally stipitate basidiocarps, with non-crustose stipe surfaces, and are distinguishable by the morphology of the pileus surface. One clade is characterized by species with hyaline to brown cutis, composed of hyaline to brown agglutinated generative hyphae. The other clade accommodates species with radially striate pileus, and lacks any distinct cutis of agglutinated hyphae. We propose Neofavolus gen. nov., typified by N. alveolaris, for the former clade, and revise the genus Favolus, typified by F. brasiliensis, for the latter clade. Neofavolus includes N. mikawai and N. cremeoalbidus sp. nov., known only from temperate eastern Asia, in addition to N. alveolaris. Favolus includes members of the Polyporus grammocephalus complex, the P. tenuiculus complex, and P. pseudobetulinus. We reveal that the polypore known as ‘P. grammocephalus’ in Asia includes F. acervatus and F. emerici (= P. grammocephalus), whereas ‘P. tenuiculus’ includes three distinct species; F. brasiliensis from tropical America, and F. spathulatus and F. roseus from tropical Asia. Detailed descriptions and illustrations are provided for the accepted species in Favolus and Neofavolus.

Both planted and natural forests provide numerous different habitats for various types of organism. After clear-cutting, differences in the restoration process of forest ecosystems, in terms of vegetation structure and woody debris, will affect the community structure of wood-inhabiting aphyllophoraceous fungi. In this study, we conducted field surveys in broad-leaved secondary forests and in planted conifer forests to examine the chronosequential pattern of fungal community development after clear-cutting and the relationships between environmental conditions and the fungal community structure in central Japan. In 2002, we collected 1476 records from 95 fungal species. Sixty-five species were recorded only in secondary forests, 17 were recorded only in planted conifer forests, and 13 were recorded in both forest types. Fungal species composition was different between the two forest types. Redundancy analysis showed that the amount of coarse woody debris in the broad-leaved secondary forests and basal area of coniferous trees in the planted forests correlated with the fungal species composition of the forests. In the broad-leaved secondary forests, species density showed significant positive correlations with stand age, and number of records and species composition changed with stand age. In the planted conifer forests, the number of records of brown rot fungi, which has a preference for conifers, was positively correlated with stand age. Our study suggested that differences in fungal community structure between the two forest types strongly reflect the preference of fungal species for different host substrates and vegetation structure, and that each forest type maintains specialists for the dominant trees. A mosaic of different forest types will promote the maintenance of high species diversity at the landscape level, as long as secondary or primary forests cover a large enough area to maintain high species diversity.

This study reports the frequency of decay (stem/butt rot) of Xylocarpus granatum trees at Hat Khanom-Mu Ko Thale Tai National Park, Nakhonsithammarat province, and other locations in Thailand, and the identification of purported causal basidiomycetes based on morphological and molecular analyses. Four survey plots at Hat Khanom-Mu Ko Thale Tai National Park were established and the incidence of butt rot determined. Percentage stem/butt rot incidence of X. granatum trees varied from 40.9 to 94.4 % with an average of 85.5 % along all four Plots. Trees in Plot 2 supported the heaviest incidence rate (94.4 %), with the lowest rate in Plot 3 (40.9 %). Ninety-two basidiomes were collected, and 46 fungal strains (50 %) isolated into axenic culture, the majority associated with tree roots (68.5 % of all collections) with 31.5 % from the tree trunks. Molecular results, based on LSU and ITS1, 2, 5.8 S rDNA analyses, confirmed that all samples belonged to the poroid genus Fulvifomes in the Hymenochaetaceae within the Hymenochaetales, Basidiomycota. The 43 specimens sequenced grouped into three clades; one clade comprised specimens isolated from only the trunks and branches (14 strains), while the remainders were from roots (29 strains) and shown to be salt tolerant. The stem/butt rot strains formed unique phylotypes which did not group with other known Fulvifomes species.

We reviewed the ecological characteristics of wood-inhabiting fungi in Malaysia in relation to the major threats to these fungi; we also examined the forest uses that would help to conserve them. Although wood-inhabiting fungi do not show high host specificity or preference in many tropical areas, several are specific to Dipterocarpaceae trees in Malaysia and some species may preferably inhabit other minor tree species. Tree size and decomposition stage are also important determinants of which fungi are present. Among the polypores described by E. J. H. Corner, 41 and 26 species have been recorded only from Malaysian lowland rainforest and montane forest, respectively. Evidence suggests that both of these forest types in Malaysia are home to unique fungal communities. More than 30 polypore species described by Corner are known only from their type localities. These species are likely rare and may be restricted to old-growth forests. Logging decreases species richness of wood-inhabiting fungi because the number of natural treefalls is decreased in logged forests, and the decline of old-growth forests is a major threat to conservation of Malaysian fungi. However, species richness of wood-inhabiting fungi is relatively high in old secondary forests and forests undergoing reduced-impact logging. The diversity of wood-inhabiting fungi is extremely low in oil palm plantations, whereas several species inhabit rubber-tree and acacia plantations. Preservation of old-growth forest is essential for conserving rare wood-inhabiting fungi in Malaysia, but old secondary forests, reduced-impact logged forests, and matured tree plantations may have some importance for the conservation of some species.

Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

A taxonomic study based on morphological and phylogenetic characters revealed that the specimens referred to as ‘Polyporus pseudobetulinus’ in Japan actually represent two distinct species, namely, P. pseudobetulinus and P. subvarius. These cam be distinguished by characteristics of the pileus surface, the presence/absence of clamp-connections on generative hyphae, and the shape of the basidiospores. P. subvarius is newly reported from Japan following the original description from China. The phylogenetic positions, detailed descriptions, and illustrations are provided for both species.

The yield-per-recruit (YPR) analysis has been used to assess growth-overfishing of exploited fish stocks. Since the ex-vessel price per weight widely depends on the size of the fish, the result of the YPR does not imply the revenue. The value-per-recruit (VPR) analysis, which is an economic expansion of the YPR analysis, was conducted for bighand thornyhead Sebastolobus macrochir caught off the Pacific coast of northern Honshu, Japan. The results showed that, under the current age at first capture (tc = 3), the current fishing mortality (F = 0.12) was close to optimum level. However, under the current F, optimum tc in the VPR model was 8 years and would lead to a 47% increase compared to the current revenue. The maximum YPR was obtained at tc = 6 years, but the revenue at tc = 6 only gave a 20% increase in the maximum revenue. The difference was caused by the size dependency of the ex-vessel price per weight. The VPR model would generate fisheries management plans with both economical and biological consideration and would help in making general consensus of fisheries management strategies., 成長乱獲診断に広く用いられているYPR解析を拡張し、単価のサイズ依存を考慮したVPR 解析を、東北海域で漁獲されたキチジのデータに対して行った。その結果、現状の漁獲開始年齢（tc=3歳）では、現状の漁獲係数（F=0.12）は、最適なYPRやVPRを概ね達成しているが、現状のFを維持した場合、最適なtcはVPR解析とYPR解析で、それぞれ8歳と6歳、またその時の収入の増加はそれぞれ47％と20％となり、結果の差異が明らかになった。VPR解析が資源管理における合意形成に寄与することが期待される。