Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants

Partial mycoheterotrophy in Apostasia wallichii, an early-diverging Asian tropical orchid

All orchids exhibit mycoheterotrophy during their early development stages, which predisposes certain species to retain this nutritional mode into adulthood. Consequently, many orchids adopt partial mycoheterotrophy, a mixotrophic strategy combining carbon acquisition through both autotrophy and mycoheterotrophy. However, whether this strategy represents an ancestral trait remains contested. This study examines the fungal symbionts and nutritional strategies of the early-diverging orchid Apostasia wallichii and a sympatric, photosynthetic orchid, Cystorchis variegata, in tropical Asia (Sabah, Malaysian Borneo). Specifically, we explored their potential nutritional modes and mycobionts by analysing δ13C and δ15N isotopic profiles and employing high-throughput DNA sequencing. Community profiling via metabarcoding revealed that the A. wallichii individuals investigated were predominantly associated with putatively saprotrophic Botryobasidium fungi, while C. variegata was simultaneously associated with non-ectomycorrhizal rhizoctonias, saprotrophic non-rhizoctonia fungi, and ectomycorrhizal fungi. Additionally, stable isotope analysis showed that both A. wallichii and C. variegata were significantly enriched in 13C and 15N compared to co-occurring autotrophic plants, indicating partial mycoheterotrophy. Our findings, particularly the discovery of partial mycoheterotrophy associated with non-ectomycorrhizal fungi in A. wallichii, suggest that partial mycoheterotrophy in green orchids may be more widespread than previously believed and could represent an ancestral trait intrinsic to orchids.

Green, variegated, and albino Cremastra variabilis provide insight into mycoheterotrophic evolution associated with wood-decaying fungi

With approximately 31,000 species, orchids begin life as mycoheterotrophs, relying on fungi to meet their carbon demands. Notably, some green orchids retain the ability to acquire carbon through fungal associations (partial mycoheterotrophy) and occasionally produce albino or, more rarely, variegated phenotypes. A linear relationship has been observed between leaf chlorophyll content and dependence on fungal-derived carbon, particularly in orchids associated with ectomycorrhizal (ECM) fungi, but whether such plasticity is similarly robust among orchids associated with non-ECM fungi remains underexplored. Here, we focused on the green, variegated, and albino forms of Cremastra variabilis, which likely lack ECM associations, to investigate (i) whether the degree of mycoheterotrophy, indicated by 13C enrichment, correlates with chlorophyll content, and (ii) whether nutritional shifts align with changes in plant structure and mycorrhizal communities. Our results show that rhizoctonia fungi were dominant in green individuals with high chlorophyll levels and lacking coralloid rhizomes, whereas albino and most variegated individuals possessing coralloid rhizomes primarily associate with Psathyrellaceae fungi. Chlorophyll content and carbon stable isotope abundances were negatively correlated, indicating a gradient of increasing mycoheterotrophy from green to albino forms in individuals with coralloid rhizomes. In conclusion, C. variabilis maintains a flexible balance between photosynthesis and mycoheterotrophy, likely shaped by its subterranean morphology and fungal associations, with wood-decaying Psathyrellaceae fungi providing greater support for mycoheterotrophic nutrition than rhizoctonia fungi.

Identification of Large Japanese field mouse Apodemus speciosus food plant resources in an industrial green space using DNA metabarcoding

DNA metabarcoding was employed to identify the food plant resources of the Large Japanese field mouse Apodemus speciosus inhabiting an artificial green space on reclaimed land on the Chita Peninsula in Aichi Prefecture, Central Japan, from 2012 to 2014. DNA metabarcoding was performed using high-throughput sequencing of partial rbcL sequences extracted from fecal samples collected in the study area. The obtained sequences, which were analyzed using a constructed local database, revealed that a total of 72 plant taxa were utilized as food plant resources by A. speciosus. Of these plant taxa, 43 could be assigned to species (59.7%), 16 to genus (22.2%), and 13 to family (18.1%). Of the 72 plant taxa identified in this study, the dominant families throughout all collection periods were Lauraceae (81.0% of 100 fecal samples), followed by Fagaceae (70.0%), Rosaceae (68.0%), and Oleaceae (48.0%). Fifty of the 72 plant taxa identified as food plant resources were woody plants. The findings showed that DNA metabarcoding using a local database constructed from the National Center for Biotechnology Information (NCBI) database and field surveys was effective for identifying the dominant food plants in the diet of A. speciosus. The results of this study provided basic information that can be applied to the formulation and implementation of management and conservation strategies for local wildlife.

Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in subtropical coastal vegetated ecosystems

In South Africa, mangrove forests and seagrass meadows often co-occur in estuarine systems and in combination host rich, often endemic biodiversity. There is an urgent need to explore community diversity in coastal vegetated ecosystems, given the degrading effects of climate change and anthropogenic pressures. Environmental DNA metabarcoding is a promising biomonitoring tool in South African coastal ecosystems, although studies highlight the need to optimise and standardise sampling protocols. This study aimed to contribute to developing sampling protocols by understanding the applicability of environmental DNA (eDNA) metabarcoding within coastal vegetated habitats and by investigating diversity using two different sample types. Aquatic and sedimentary environmental DNA samples from three estuaries along the east coast of South Africa, in combination with MiFish metabarcoding, detected 148 operational taxonomic units (OTUs) representing 67 fish genera from 50 families, although only 16% were resolved to species. We observed that aquatic eDNA samples detected 97% of the total fish diversity, suggesting that this is an efficient tool to comprehensively detect ichthyofaunal diversity. We did not detect different fish communities between mangroves and seagrasses and our findings underscore the importance of taking hydrological connectivity into consideration for sampling design. Overall, our work reinforces key considerations for future eDNA metabarcoding studies focused on fish fauna in estuaries, and therefore contributes to optimising sampling protocols to support the biomonitoring of coastal biodiversity.

High mycorrhizal specificity in the monotypic mycoheterotrophic genus Relictithismia (Thismiaceae)

Mycoheterotrophic plants, which depend entirely on mycorrhizal fungi for carbon acquisition, often exhibit high specificity toward their fungal partners. Members of Thismiaceae are generally recognized for their extreme mycorrhizal specialization and rarity. In this study, we examined the mycorrhizal associations of Relictithismia, a recently discovered monotypic genus within Thismiaceae, and Thismia abei, a Thismia species with a similar distribution in southern Japan, by employing high-throughput DNA sequencing of the 18S rRNA gene. Our analyses revealed that both R. kimotsukiensis and T. abei are predominantly associated with two specific virtual taxa (VTX00295 and VTX00106) of the genus Rhizophagus (Glomeraceae). These shared associations may reflect either phylogenetic niche conservatism, in which the common ancestor of R. kimotsukiensis and T. abei retained the same AM fungal partners, or convergent evolution, in which the AM fungal phylotypes were independently recruited due to their potential benefits for these mycoheterotrophic plants. Furthermore, BLAST searches demonstrated that VTX00295 and VTX00106 are widely distributed globally, suggesting that highly specialized mycorrhizal interactions are unlikely to be the primary drivers of the limited distribution and rarity of R. kimotsukiensis and T. abei. Overall, our findings enhance our understanding of high mycorrhizal specificity in Thismiaceae. However, broader investigations, combining extensive sampling of Thismiaceae species with ancestral state reconstruction, are needed to determine whether the shared associations detected here reflect phylogenetic niche conservatism or convergent evolution.

Extending the Influence of Terroir through the Spontaneous Fermentation of Pinot Noir in the Vineyard: A Case Study of Greystone Vineyard Fermentation

This study investigates the influence of vintage and fermentation environment on the microbial diversity, chemical composition, and volatile profiles of Pinot Noir wines, with a focus on comparing vineyard (outdoor) and winery (indoor) fermentations across two consecutive vintages, 2019 and 2020. Grapes were hand-harvested from a single vineyard and subjected to spontaneous fermentations in three tanks for each fermentation environment. Nonmetric multidimensional scaling (NMDS) and PERMANOVA analyses revealed significant differences in fungal community composition between fermentation environments and vintages. Vineyard fermentations consistently exhibited higher levels of non-Saccharomyces yeasts during fermentation, which contributed to increased production of microbial-derived esters, such as hexyl acetate and isobutyl acetate. Winery fermentations, in contrast, showed higher concentrations of anthocyanins, contributing to enhanced color intensity and stability. Vintage effects were more evident than fermentation environment, with the 2019 vintage favoring higher concentrations of phenolics, anthocyanins, higher alcohols (e.g. isoamyl alcohol), and volatile phenols (e.g. guaiacol and eugenol), while the 2020 vintage enhanced the retention of esters and floral terpenes (e.g. linalool). These findings highlight the distinct wine styles achievable through vineyard and winery fermentations, as well as the interplay between climatic conditions and fermentation environment. This work provides novel insights into the potential of vineyard fermentations for expressing microbial terroir and offers practical strategies for optimizing wine production under varying climatic and site-specific conditions.

Reduction of the α and β diversity of ectomycorrhizal fungal community under snowmelt: highlights from a common garden trial using Abies sachalinensis with differing host origins and light condition

The community structure of ectomycorrhizal (ECM) fungi typically displays temporal dynamics. However, heavy snow cover hinders belowground investigations in temperate-to-boreal forests where ECM trees dominate, and the dynamics of the ECM fungal community structure during winter have not been fully elucidated. Given that boreal conifer species start root production in response to snowmelt, studies on the response of the ECM fungal community to snowmelt are needed. In the present study, to infer the community dynamics during the snowmelt season and their susceptibility to host tree conditions, we investigated ECM fungi associated with saplings of the evergreen conifer Abies sachalinensis immediately after the start and end of snowmelt in a common garden experiment. Saplings derived from two sources of contrasting snowfall conditions (heavy vs. little) were grown under two different light conditions (open vs. shaded), and the ECM fungal community dynamics patterns were compared across these combinations. The response of the ECM fungal community structure varied across treatments; although significant loss of ECM fungal operational taxonomic units (OTUs) was observed when saplings from the heavy snowfall region were grown under shade conditions, no change in community structure across the snowmelt season was observed for the other combinations. The stability of community composition despite the change in abiotic conditions with snowmelt, together with the effects of host origin and light conditions on community dynamics patterns, would imply the importance of host-mediated community dynamics of ECM fungi during the snowmelt season.

The tiny-leaved orchid Disperis neilgherrensis primarily obtains carbon from decaying litter via saprotrophic Ceratobasidium

While most green orchids establish associations with non-ectomycorrhizal rhizoctonias belonging to Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae, fully mycoheterotrophic orchids-excluding albino mutants-primarily depend on either ectomycorrhizal fungi or saprotrophic non-rhizoctonia fungi. This suggests that non-ectomycorrhizal rhizoctonias may be unable to meet the carbon demands of adult orchids that exhibit a high degree of mycoheterotrophy. To understand the physiological ecology of Disperis neilgherrensis, an orchid species with reduced leaves growing in decaying litter from non-ectomycorrhizal trees, we employed molecular and stable isotope analyses to identify its mycorrhizal partners and ultimate nutritional sources at two populations on Ishigaki Island, Japan. Molecular barcoding techniques revealed that D. neilgherrensis forms exclusive associations with non-ectomycorrhizal Ceratobasidiaceae fungi. The Disperis specimens exhibited δ13C and δ15N isotopic values similar to those found in fully mycoheterotrophic orchids that exploit litter-decaying fungi. Furthermore, the pelotons of D. neilgherrensis showed significantly elevated δ13C values similar to saprotrophic non-rhizoctonia fungi. Our findings indicate that D. neilgherrensis primarily obtains its carbon from decaying litter through a specialized relationship with non-ECM Ceratobasidiaceae. Given that saprotrophic Ceratobasidiaceae facilitate nearly fully mycoheterotrophic growth in D. neilgherrensis, at least under warm and humid conditions, it is plausible that other (nearly) fully mycoheterotrophic tropical orchids also meet their carbon requirements through associations with saprotrophic rhizoctonias.

Two new species of the Entoloma quadratum–Murrayi complex in Japan

We describe two new species, Entoloma. kermesinum sp. nov. and E. flavescens sp. nov., which are confused with E. quadratum and E. murrayi, respectively. We sequenced the large subunit of mitochondrial ribosomal RNA, the nuclear ribosomal internal transcribed spacer region and 22 single-copy genes for 51 specimens of E. kermesinum, E. flavescens, E. album, and related species. Species boundaries were assessed using the molecular phylogenetics and population genetics approaches. Specimens of E. kermesinum, E. flavescens, and E. album formed independent clades, which were phylogenetically distinct from the specimens of E. quadratum and E. murrayi collected around the type locality (i.e., New England). Although the phylogenetic distance between E. flavescens and E. album was small, gene flow between them was restricted in areas where they coexisted, suggesting reproductive isolation. Therefore, these five species can be treated as independent species. We found characteristics useful for identifying E. kermesinum and E. flavescens. In particular, E. kermesinum is characterized by a crimson to brown-red and fibrillose pileus, finely covered by whitish fibrous scales; E. flavescens is characterized by a lemon-yellow to tan and shiny-to-silky pileus. In addition, relatively large basidiospores and clamp connections are diagnostic features of these two species.

Drastic mycorrhizal community shifts in Sceptridium ferns during the generation transition from fully mycoheterotrophic gametophytes to photosynthetic sporophytes

Many plant species experience a prolonged subterranean phase during which they rely entirely on mycorrhizal fungi for carbon. While this mycoheterotrophic strategy spans liverworts, lycophytes, and ferns, most empirical research has centered on angiosperms. This study explores the fungal associations of Sceptridium (Ophioglossaceae), an early-diverging fern with mycoheterotrophic gametophytes. We analyzed germination patterns and fungal associations in Sceptridium gametophytes, comparing them to the distribution and mycorrhizal partners of photosynthetic sporophytes. High-throughput sequencing data reveal that mycoheterotrophic gametophytes consistently associate with a single Entrophospora fungus in the order Entrophosporales (Glomeromycotina), while photosynthetic sporophytes primarily partner with fungi from Glomeraceae (Glomerales, Glomeromycotina). Consequently, gametophytes exhibit spatial clustering without association with adult plants. This is the first documentation of an association between Entrophosporaceae (and the order Entrophosporales) and mycoheterotrophic plants. The drastic shifts in Sceptridium mycorrhizal communities across life stages likely reflect changing physiological needs during development. Further research is essential to determine whether the association with Entrophosporaceae is widespread among mycoheterotrophic species and to elucidate the functional and physiological mechanisms underlying these mycorrhizal shifts.

Subterranean morphology underpins the degree of mycoheterotrophy, mycorrhizal associations, and plant vigor in a green orchid Oreorchis patens

The evolution of full heterotrophy is a fascinating topic in plant evolution, with recent studies suggesting that partial mycoheterotrophy (mixotrophy) serves as a transitional stage toward full mycoheterotrophy in orchids. However, the adaptive significance of fungal-derived carbon in mixotrophic plants remains largely unexplored. In this study, we investigated the photosynthetic orchid Oreorchis patens, a species related to the leafless genus Corallorhiza within the subtribe Calypsoinae. Using high-throughput DNA sequencing, 13C and 15N isotopic analyses, and phenotypic evaluations, we explored the role of coralloid rhizomes - a feature common in fully mycoheterotrophic orchids - in fungal partnerships, the degree of mycoheterotrophy, and plant vigor. Our findings reveal that O. patens plants with coralloid rhizomes predominantly associate with saprotrophic Psathyrellaceae fungi, whereas those without coralloid rhizomes also partner with rhizoctonias and other potentially orchid mycorrhizal fungi. Notably, plants with coralloid rhizomes exhibited enriched 13C signatures, indicating a greater reliance on fungal-derived carbon. These plants also demonstrated more vigorous flowering scapes and produced a higher number of flowers, suggesting that mycoheterotrophy significantly enhances plant vigor. This study provides rare insights into the adaptive significance of mycoheterotrophy. Recent research suggests that some partially mycoheterotrophic orchids can adjust their heterotrophic status to optimize carbon resource use under specific conditions, such as low-light environments. However, an increased proportion of fungal-derived carbon may sometimes merely reflect reduced photosynthesis in such conditions, thereby amplifying the apparent contribution of fungal-derived carbon. Our findings offer more direct evidence that carbon acquisition via mycoheterotrophy is beneficial for partially mycoheterotrophic orchids.

Biodiversity and Bioprospecting of Fungal Endophytes from Houttuynia cordata Thunb. as a Potential Antibacterial and Anticancer Agent

Endophytic fungi are considered a new source of bioactive compounds that have important applications in agriculture and medicine. This study aims to investigate the biodiversity and potential of endophytic fungi isolated from Houttuynia cordata Thunb. as antimicrobials and anticancer agents. Out of ten isolated endophytes, four species have never been reported to be associated with H. cordata: Ceratobasidium sp., Cladosporium sp., Phomopsis sp., and Fusarium sp. The antibacterial activity assay revealed that the ethyl acetate extract of Ceratobasidium sp. HCS-3 possessed most potent antibacterial activity against Escherichia coli and Staphylococcus aureus. In addition, its cytotoxic activity test showed the promising anticancer activity on lung cancer A549, osteosarcoma MG-63, and cervical cancer HeLa cells with IC50 of 4.55±1.16, 32.14±2.78, and 1.54±0.66 ppm, respectively. Furthermore, metabolite profiling identified 66 compounds suggesting that benzoic acid, farnesol, and cyclopeptides may contribute to the antibacterial activity, while 4-methoxycinnamic acid may have anticancer potential.

Morphological and DNA analysis of pollen grains on butterfly individuals reveal their flower visitation history

Many butterfly species are conspicuous flower visitors. However, understanding their flower visitation patterns in natural habitats remains challenging due to the difficulty of tracking individual butterflies. Therefore, we aimed at establishing a protocol to solve the problem using the Common five-ring butterfly, Ypthima argus (Nymphalidae: Satyrinae). Focusing on the pollen grains attached the butterfly's body surface, we examined validities of two pollen analyses based on pollen morphology and DNA markers (ITS1 and ITS2), in addition to the classical route census method. We captured thirty-nine butterflies from mid-April to early July and collected pollen grains from each individual. Morphological and DNA analyses of collected pollens identified eighteen and thirty-four taxa of insect pollinated plants respectively, including woody plants such as Castanopsis. The DNA analysis detected as many as thirteen plant taxa from a single butterfly, indicating its high sensitivity for detecting flower visitation. We detected more plant taxa in May when many individuals were flying. This is assumingly related to the post emergence days of the butterflies with more foraging experience. We also found that fluctuations of pollen grain numbers of Leucanthemum vulgare and Erigeron philadelphicus on individual butterflies depend on their flowering periods overlapping partly. Consequently, we conclude that pollen morphology and DNA barcoding analysis, and field observations are mutually complementary techniques, providing an integrated pollen analysis method to study the pollination ecology of butterflies.

Analysis of Bacterial and Fungal Communities and Organic Acid Content in New Zealand Lambic-Style Beers: A Climatic and Global Perspective

Beer produced by autochthonous microbial fermentation is a long-established craft beer style in Belgium that has now been implemented commercially in New Zealand. We used a metabarcoding approach to characterize the microbiome of 11 spontaneously fermented beers produced by a single brewery in Oamaru from 2016 to 2022. Key organic acid concentrations were also determined. Both bacterial and fungal populations varied considerably between vintages and between individual brews produced in 2020. Similarly, for organic acids, the concentrations of L-malic acid, succinic acid, and L-lactic acid statistically differed from one vintage to another. Moreover, a correlation between the concentrations of certain organic acids and microbial composition was inferred by ordination analyses. Through reference to publicly available climate data, humidity and maximum temperature seemed to enhance the abundance of Penicillium and Hanseniaspora in beer microbiota. However, comparison with previously published studies of Belgian lambic beers, similar Russian ales, and publicly available temperature data from these regions showed that the microbial populations of these were relatively stable despite greater extremes of weather. Our results suggest that while climatic variables may influence microbial populations during beer making that employs autochthonous fermentation in New Zealand, such variation is not evident where similar beers are produced in facilities with a long-established history of production. These findings have implications for lambic-style beer production in the context of global climate change, notably where microbial populations may lack environmental adaptation.

Two waves of photosymbiosis acquisition in extant planktonic foraminifera explained by ecological incumbency

Photosymbiosis, a mode of mixotrophy by algal endosymbiosis, provides key advantages to pelagic life in oligotrophic oceans. Despite its ecological importance, mechanisms underlying its emergence and association with the evolutionary success of photosymbiotic lineages remain unclear. We used planktonic foraminifera, a group of pelagic test-forming protists with an excellent fossil record, to reveal the history of symbiont acquisition among their three main extant clades. We used single-cell 18S rRNA gene amplicon sequencing to reveal symbiont identity and mapped the symbiosis on a phylogeny time-calibrated by fossil data. We show that the highly specific symbiotic interaction with dinoflagellates emerged in the wake of a major extinction of symbiont-bearing taxa at the end of the Eocene. In contrast, less specific and low-light-adapted symbioses with pelagophytes emerged 20 million years later, in multiple independent lineages in the Late Neogene, at a time when the vertical structure of pelagic ecosystems was transformed by global cooling. We infer that in foraminifera, photosymbiosis can evolve easily and that its establishment leads to diversification and ecological dominance to such an extent, that the proliferation of new symbioses is prevented by the incumbent lineages.

Oak Wilt Disease May Reduce the Initial Decay Rate of Dead Quercus serrata Stems by Altering Fungal Communities in the Wood

Oak wilt causes severe dieback of Quercus serrata, a dominant tree species in the lowlands across Japan. This study evaluated the effects of oak wilt on the wood-inhabiting fungal community and the decay rate of deadwood using a field monitoring experiment. We analysed the fungal metabarcoding community from 1200 wood samples obtained from 120 experimental logs from three forest sites at five different time points during the initial 1.5 years of the experiment. Death due to wilt significantly influenced the fungal community composition and reduced fungal diversity, likely due to the dominance of a limited number of species. The operational taxonomic unit richness, occurrence frequency, and DNA copy number of white rot fungi were also enhanced on the logs killed by wilt, depending on the sites. Structural equation modelling suggested that the wilt-initiated changes in the fungal community reduced the decay rate of oak logs. Temperature and wood moisture also affected the fungal community and log decomposition. These results suggest that, in addition to the direct effect of climate, oak wilt indirectly affects log decomposition by structuring the fungal community. Continuous monitoring is essential to evaluate the longer-term effects of oak wilt on the fungal decomposition of wood.

Evaluation of the persistence of Epichloë endophyte and its possible effect on fungal assemblages in dead leaf sheaths

The systemic fungal endophytes of the genus Epichloë inhabit the aerial part of host grasses. Recent studies have reported that Epichloë affects the non-systemic endophytic assemblages in live leaves, but few studies that have demonstrated the occurrence of Epichloë and its effect on fungal assemblages in dead leaves. We proposed a hypothesis that Epichloë decreases from live to dead leaves but affects the non-systemic endophytic assemblages also in dead leaves. To test this hypothesis, we sampled leaf sheaths from four leaf types (live, senescent, attached dead and fallen dead) of two native grass species Elymus racemifer and Elymus tsukushiensis var. transiens in Japan and assessed for fungi by DNA metabarcoding. The occurrence of Epichloë OTU was significantly greater in E. tsukushiensis var. transiens than in E. racemifer and varied significantly between the four-leaf types, with decreased and no detections in attached dead and fallen dead leaves, respectively. The composition of non-systemic endophytic assemblages was also significantly affected by the presence/absence of Epichloë OTU, leaf type, host grass species and their interactions. These results supported our hypothesis and suggested that Epichloë can indirectly lead to the changes in belowground processes such as litter decomposition by affecting saprotrophic fungi in dead leaves.

Insular environment-dependent introgression from an arid-grassland orchid to a wetland orchid on an oceanic island

Adaptive introgression plays a vital role in allowing recipient species to adapt and colonize new environments. However, our understanding of such environment-dependent introgressions is primarily limited to specific plant taxa in particular settings. In Japan, two related orchid species, the autonomously self-pollinating Pogonia minor and the outcrossing Pogonia japonica, typically inhabit dry grasslands and wetlands, respectively. Intriguingly, an island ecotype of P. japonica exists in arid, wind-swept, open sites on volcanic mountain slopes on Kozu Island, in the oceanic Izu Islands. To investigate potential introgression and its implications between P. japonica and P. minor on Kozu Island, we applied a comprehensive approach that included examining morphological traits, genome-wide SNP data, and plastid DNA sequences. We also examined the breeding systems of these species on Kozu Island through artificial pollination experiments to determine if introgression from P. minor has endowed the P. japonica ecotype with selfing capabilities. Extensive sampling on Kozu Island revealed that all P. japonica specimens exhibit signs of introgression from P. minor, suggesting the absence of pure P. japonica populations on the island. Furthermore, the chloroplast haplotypes of the insular P. japonica ecotype consistently match those of P. minor, indicating a predominantly asymmetrical initial hybridization with P. minor acting mainly as the maternal parent in the formation of F1 hybrids. Despite the advantages of self-fertilization in isolated environments, the insular P. japonica does not exhibit autogamy. Consequently, the scarcity of moist habitats, rather than selection pressure for selfing, likely contributes to the observed widespread introgression. Our study strongly suggests that the arid-environment-adapted P. minor has introgressed into the insular ecotype of P. japonica, enabling its successful colonization of arid volcanic mountain slopes of the oceanic island.

Diversity of ligninolytic ascomycete fungi associated with the bleached leaf litter in subtropical and temperate forests

Little is known regarding the diversity patterns of Xylariaceae and Hypoxylaceae (Ascomycota) fungi taking part in the lignin decomposition of leaf litter from different tree species and under different climatic regions. The alpha and beta diversity of Xylariaceae and Hypoxylaceae fungi was investigated on bleached leaf litter from nine subtropical and cool temperate tree species in Japan. A total of 248 fungal isolates, obtained from 480 leaves from the nine tree species, were classified into 43 operational taxonomic units (OTUs) with a 97% similarity threshold and were assigned to nine genera of Xylariaceae and Hypoxylaceae. There was no overlap of fungal OTUs between subtropical and cool temperate trees. The mean number of fungal OTUs was generally higher in subtropical than cool temperate trees, whereas rarefaction curves depicting the numbers of OTU with respect to the number of leaves from which fungi were isolated were less steep in subtropical trees than in cool temperate trees, reflecting the dominance of major OTUs in the subtropical trees and indicating a higher species richness in cool temperate regions. Nonmetric multidimensional scaling showed general overlaps of fungal OTU compositions among tree species in the respective climatic regions, and one-way permutational multivariate analysis of variance indicated that the OTU composition was not significantly different between the tree species. These results suggest a wide host range and some geographic and climatic structures of distribution of these ligninolytic fungi.

Legionella community dynamics in a drinking water distribution system: Impact of residual chlorine depletion

This study investigated the occurrence of Legionella spp. in a chlorinated drinking water distribution system (DWDS), focusing on their community compositions and association with physicochemical water quality. Water samples were collected throughout the DWDS, covering from the treated water reservoir to distal ends. Although Legionella spp. genes were not detected at the reservoir, their abundance dramatically increased along the distribution network, reaching up to 4.4 log copies/L at distal sites. The Legionella communities were further characterized by high-throughput amplicon sequencing targeting the genus-specific 16S rRNA gene. The results revealed a diverse Legionella community, including amplicon sequence variants with high similarity (> 99 %) to potentially pathogenic species such as L. drozanskii and L. pneumophila, albeit at low levels. Moreover, Legionella community diversity increased significantly along the distribution system, leading to distinct community compositions at distal sites. Importantly, decay of residual chlorine concentration was identified as a key factor both in increasing the Legionella gene levels and shaping the community structure. Overall, this study underscores the importance of preventing pipe corrosion and maintaining adequate disinfectant residuals to minimize Legionella regrowth in DWDS.

Mycorrhizal and endophytic fungi structure forest below-ground symbiosis through contrasting but interdependent assembly processes

BACKGROUND

Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus-fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont-symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus-fungus associations by a statistical modeling that could account for implicit environmental effects.

RESULTS

The fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus-fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus-fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.

CONCLUSION

By applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus-fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant-fungal symbiosis.

phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.

Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing

Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.

Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment

Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.

Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas

Background

Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection.

Methods

Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection.

Results and Discussion

This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection.

Conclusion

We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.

Foraging ants affect community composition and diversity of phyllosphere fungi on a myrmecophilous plants, Mallotus japonicus

Many microorganisms inhabit the aboveground parts of plants (i.e. the phyllosphere), which mainly comprise leaves. Understanding the structure of phyllosphere microbial communities and their drivers is important because they influence host plant fitness and ecosystem functions. Despite the high prevalence of ant-plant associations, few studies have used quantitative community data to investigate the effects of ants on phyllosphere microbial communities. In the present study, we investigated the effects of ants on the phyllosphere fungal communities of Mallotus japonicus using high-throughput sequencing. Mallotus japonicus is a myrmecophilous plants that bears extrafloral nectaries, attracting several ant species, but does not provide specific ant species with nest sites like myrmecophytes do. We experimentally excluded ants with sticky resins from the target plants and collected leaf discs to extract fungal DNA. The ribosomal DNA internal transcribed spacer 1 (ITS1) regions of the phyllosphere fungi were amplified and sequenced to obtain fungal community data. Our results showed that the exclusion of ants changed the phyllosphere fungal community composition; however, the effect of ants on OTU richness was not clear. These results indicate that ants can change the community of phyllosphere fungi, even if the plant is not a myrmecophyte.

Transmission dynamics of symbiotic protist communities in the termite gut: association with host adult eclosion and dispersal

The fidelity of vertical transmission is a critical factor in maintaining mutualistic associations with microorganisms. The obligate mutualism between termites and intestinal protist communities has been maintained for over 130 million years, suggesting the faithful transmission of diverse protist species across host generations. Although a severe bottleneck can occur when alates disperse with gut protists, how protist communities are maintained during this process remains largely unknown. In this study, we examined the dynamics of intestinal protist communities during adult eclosion and alate dispersal in the termite Reticulitermes speratus. We found that the protist community structure in last-instar nymphs differed significantly from that in workers and persisted intact during adult eclosion, whereas all protists disappeared from the gut during moults between worker stages. The number of protists in nymphs and alates was substantially lower than in workers, whereas the proportion of protist species exhibiting low abundance in workers was higher in nymphs and alates. Using a simulation-based approach, we demonstrate that such changes in the protist community composition of nymphs and alates improve the transmission efficiency of whole protist species communities. This study thus provides novel insights into how termites have maintained mutualistic relationships with diverse gut microbiota for generations.

Spread of antibiotic resistance genes to Antarctica by migratory birds

Recent studies have highlighted the presence of antibiotic resistance genes (ARGs) in Antarctica, which are typically indicative of human activity. However, these studies have concentrated in the Antarctic Peninsula region, and relatively less is known about ARG prevalence in East Antarctica, where human activity levels are lower compared to the Antarctic Peninsula. In addition, the mechanisms of ARG transmission to Antarctica through natural or anthropogenic pathways remain unclear. In this study, we analyzed the fecal samples of Adélie penguins and South polar skuas by using high-throughput sequencing and microfluidic quantitative PCR to detect potential pathogens and ARGs at their breeding colonies near Syowa Station in East Antarctica. These results revealed the presence of several potential pathogens in the fecal matter of both bird species. However, the HF183 marker, which indicates human fecal contamination, was absent in all samples, as well as seawater sampled near the breeding colonies. This suggests that the human fecal contamination was negligible in our study area. In addition to pathogens, we found a significant number of ARGs and metal resistance genes in the feces of both Adélie penguins and South polar skuas, with higher detection rates in skuas than in penguins. To better understand how these birds acquire and transmit these genes, we analyzed the migratory patterns of Adélie penguins and South polar skuas by geolocator tracking. We found that the skuas migrate to the tropical and subtropical regions of the Indian Ocean during the austral winter. On the other hand, Adélie penguins exhibited a more localized migration pattern, mainly staying within Antarctic waters. Because the Indian Ocean is considered one of the major reservoirs of ARGs, South polar skuas might be exposed to ARGs during their winter migration and transfer these genes to Antarctica.

Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Partial mycoheterotrophy in the leafless orchid Eulophia zollingeri specialized on wood-decaying fungi

Although the absence of normal leaves is often considered a sign of full heterotrophy, some plants remain at least partially autotrophic despite their leafless habit. Leafless orchids with green stems and capsules probably represent a late evolutionary stage toward full mycoheterotrophy and serve as valuable models for understanding the pathways leading to this nutritional strategy. In this study, based on molecular barcoding and isotopic analysis, we explored the physiological ecology of the leafless orchid Eulophia zollingeri, which displays green coloration, particularly during its fruiting phase. Although previous studies had shown that E. zollingeri, in its adult stage, is associated with Psathyrellaceae fungi and exhibits high 13C isotope signatures similar to fully mycoheterotrophic orchids, it remained uncertain whether this symbiotic relationship is consistent throughout the orchid's entire life cycle and whether the orchid relies exclusively on mycoheterotrophy for its nutrition during the fruiting season. Our study has demonstrated that E. zollingeri maintains a specialized symbiotic relationship with Psathyrellaceae fungi throughout all life stages. However, isotopic analysis and chlorophyll data have shown that the orchid also engages in photosynthesis to meet its carbon needs, particularly during the fruiting stage. This research constitutes the first discovery of partial mycoheterotrophy in leafless orchids associated with saprotrophic non-rhizoctonia fungi.

Geographical variation of bacterial and ciliophoran communities in tidal flats in a continental archipelago

In tidal flats, which are located at the transition zone between terrestrial and marine ecosystems, environmental factors such as temperature, sediment particle size, and tidal range exhibit geographic variation. Accordingly, the composition and structure of the microbial communities in the tidal flats are likely to vary in geographically different habitats. To clarify these differences with environmental factors causing them, we analyzed microbial communities consisting of bacteria and ciliates in sediments collected from nine tidal flats in geographical diverse region from Hokkaido to Kagoshima, Japan. The results confirmed that the community structures of bacteria and ciliophora in tidal flat sediments differed at the geographical scale of the Japanese archipelago. However, the variation could not be explained by the physical distance between the tidal flats nor by the differences in the trophic conditions among the tidal flats. Instead, the OTU richness of both the bacterial and ciliophoran communities was significantly related to the tidal range. The results also showed that bacteria and ciliophora tended to form similar communities among the tidal flats with similar median particle sizes. Furthermore, ciliophoran communities were similar among the tidal flats with similar bacterial communities. The results suggest that bacteria and ciliophora interact each other through trophic relationships or physical and chemical processes in the sediment habitats.

Influence of climatic variation on microbial communities during organic Pinot noir wine production

To assess the possible impact of climatic variation on microbial community composition in organic winemaking, we employed a metabarcoding approach to scrutinize the microbiome in a commercial, organic, Pinot noir wine production system that utilizes autochthonous fermentation. We assessed microbial composition across two vintages (2018 and 2021) using biological replicates co-located at the same winery. Microbial dynamics were monitored over four important fermentation time points and correlated with contemporaneous climate data. Bacterial (RANOSIM = 0.4743, p = 0.0001) and fungal (RANOSIM = 0.4738, p = 0.0001) compositions were different in both vintages. For bacteria, Lactococcus dominated the diversity associated with the 2018 vintage, while Tatumella dominated the 2021 vintage. For fungal populations, while Saccharomyces were abundant in both vintages, key differences included Starmerella, copious in the 2018 vintage; and Metschnikowia, substantive in the 2021 vintage. Ordination plots correlated the climatic variables with microbial population differences, indicating temperature as a particularly important influence; humidity values also differed significantly between these vintages. Our data illustrates how climatic conditions may influence microbial diversity during winemaking, and further highlights the effect climate change could have on wine production.

Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake

Viruses infect and kill prokaryotic populations in a density- or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and de-stratified periods, on the changes in prokaryotic and viral communities and their interactions remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic and viral community composition. Our analysis revealed that, in the surface layer, 19 prokaryotic species, accounting for approximately 40% of the total prokaryotic abundance, could potentially contribute to the majority of prokaryotic production, which is the highest during the summer and is suppressed by viruses. This suggests that a small fraction of prokaryotes and phages were the key infection pairs during the peak period of prokaryotic activity in the freshwater lake. We also found that approximately 50% of the dominant prokaryotic and viral species in the deep layer were present throughout the study period. This suggests that the "kill the winner" model could explain the viral impact on prokaryotes in the surface layer, but other dynamics may be at play in the deep layer. Furthermore, we found that annual vertical mixing could result in a similar rate of community change between the surface and deep layers. These findings may be valuable in understanding how communities and the interaction among them change when freshwater lake stratification is affected by global warming in the future.IMPORTANCEViral infection associated with prokaryotic production occurs in a density- or frequency-dependent manner and regulates the prokaryotic community. Stratification transition and annual vertical mixing in freshwater lakes are known to affect the prokaryotic community and the interaction between prokaryotes and viruses. By pairing measurements of virome analysis and prokaryotic production of a 1-year survey of the depths of surface and deep layers, we revealed (i) the prokaryotic infection pairs associated with prokaryotic production and (ii) the reset in prokaryotic and viral communities through annual vertical mixing in a freshwater lake. Our results provide a basis for future work into changes in stratification that may impact the biogeochemical cycling in freshwater lakes.

Elevated abundance of Komagataeibacter results in a lower pH in kombucha production; insights from microbiomic and chemical analyses

Kombucha consumption has grown rapidly worldwide in the last decade, with production at both small- and large scales. The complex fermentation process involves both bacterial and yeast species, but little is known regarding the progression of microbial development during production. We explored the microbial diversity of multiple batches across two kombucha types, i. e commercial scale versus laboratory-made (hereafter "home") kombucha brew using metabarcoding to characterize both fungal and bacterial communities. We found the microbial community of the commercial kombucha brew to be more complex than that of the home brew. Furthermore, PERMANOVA uncovered significant compositional differences between the bacterial (F = 2.68, R2 = 0.23, p = 00.001) and fungal (F = 3.18, R2 = 0.26, p = 00.006) communities between batches. For the home brew, both alpha and beta diversity analyses revealed no significant differences between all batches and replicates. When the microbial diversity of the home and commercial kombucha types were directly compared, the former had higher proportions of Ammoniphilus and Komagataeibacter. The commercial kombucha on the other hand were high in Anoxybacillus, Methylobacterium and Sphingomonas. For the fungal communities, the most dominant fungal genera detected in both kombucha types were similar. Linear model revealed significant correlations between some microorganisms and the sugars and organic acids assayed in this study. For example, rising glucose levels correlated with an increase in the relative abundance of Komagataeibacter (F = 7.115, Adj. R2 = 0.44, p = 00.0003). We believe these results contribute towards achieving a better control of the kombucha fermentation process and may assist in targeted product diversification.

The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes

Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.

DNA metabarcoding focusing on the plankton community: an effective approach to reconstruct the paleo-environment

DNA metabarcoding (DNA-MB) targeting the whole plankton community is a promising approach in studies of sediment samples from water bodies, but its effectiveness in ancient material is not well demonstrated. We applied DNA-MB of plankton in a sediment core to reconstruct the paleo-environment of Lake Shinji, Japan, through a marine lagoon/freshwater lake transition during the past 2300 years. We interpreted core-sample plankton taxonomy and habitat by reference to the modern plankton community in water samples. OTUs (operational taxonomic units) belonging to Dictyochophyceae were 81.05% of the total reads in sediments. However, Ciliophora, Copepoda and Labyrinthulea formed the majority of plankton taxa in the water samples, suggesting that they are under-represented in sediment. A drastic change in plankton composition correlated with a large decrease in sediment sulfur concentration, implying the change of aquatic environment from marine lagoon to freshwater lake. This event took place ca. 1200 CE in Lake Shinji. A 250 year-long transitional period followed, during which the total DNA sequence reads were very low. This suggests that salinity fluctuations created a hostile environment for both marine and freshwater plankton species. Our results show that DNA-MB of the whole plankton community is effective in reconstructing paleo-environments.

Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes

Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by faecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We examined 420 faecal samples and found different patterns of dietary diversity and composition among the duck species. The pattern also differed between plant and invertebrate food. Dietary niche partitioning was clear in plant food. Large-bodied ducks intensively use crop plants, and other ducks might mediate competition by using terrestrial and aquatic plants that are suitable for their foraging behaviours or microhabitats. Dietary segregation among species was the most apparent in February, when the abundance of foraging ducks was the largest. This study illustrated the complex pattern of dietary niche partitioning of dabbling ducks in agricultural landscapes, which might be difficult to evaluate by conventional approaches. The availability of crop plants, as well as other plant food resources in flooted areas and farmland dikes, may enable ducks to coexist by spatial or behavioural resource partitioning.

DNA metabarcoding focused on difficult-to-culture protists: An effective approach to clarify biological interactions

DNA metabarcoding on a single organism is a promising approach to clarify the biological interactions (e.g., predator-prey relationships and symbiosis, including parasitism) of difficult-to-culture protists. To evaluate the effectiveness of this method, Radiolaria and Phaeodaria, which are ecologically important protistan groups, were chosen as target taxa. DNA metabarcoding on a single organism focused on the V9 region of the 18S rRNA gene revealed potential symbionts, parasites and food sources of Radiolaria and Phaeodaria. Previously reported hosts and symbionts (parasites) were detected, and newly recognized combinations were also identified. The contained organisms largely differed between Radiolaria and Phaeodaria. In Radiolaria, members of the same order tended to contain similar organisms, and the taxonomic composition of possible symbionts, parasites, and food sources was fixed at the species level. Members of the same phaeodarian family, however, did not contain similar organisms, and body part (i.e., the central capsule or the phaeodium) was the most important factor that divided the taxonomic composition of detected organisms, implying that the selection of appropriate body part is important when trying to ascertain contained organisms, even for unicellular zooplankton. Our results show that DNA metabarcoding on a single organism is effective in revealing the biological interactions of difficult-to-culture protists.

Phylogeny-based assignment of functional traits to DNA barcodes outperforms distance-based, in a comparison of approaches

The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach.

An ecological network approach for detecting and validating influential organisms for rice growth

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence the rice performance in the field has been underexplored despite the potential of ecological communities to establish an environment-friendly agricultural system. In the present study, we demonstrate an ecological-network-based approach to detect potentially influential, previously overlooked organisms for rice (Oryza sativa). First, we established small experimental rice plots, and measured rice growth and monitored ecological community dynamics intensively and extensively using quantitative environmental DNA metabarcoding in 2017 in Japan. We detected more than 1000 species (including microbes and macrobes such as insects) in the rice plots, and nonlinear time series analysis detected 52 potentially influential organisms with lower-level taxonomic information. The results of the time series analysis were validated under field conditions in 2019 by field manipulation experiments. In 2019, we focused on two species, Globisporangium nunn and Chironomus kiiensis, whose abundance was manipulated in artificial rice plots. The responses of rice, namely, the growth rate and gene expression patterns, were measured before and after the manipulation. We confirmed that, especially in the G. nunn-added treatment, rice growth rate and gene expression pattern were changed. In the present study, we demonstrated that intensive monitoring of an agricultural system and the application of nonlinear time series analysis were helpful to identify influential organisms under field conditions. Although the effects of the manipulations were relatively small, the research framework presented here has future potential to harness the ecological complexity and utilize it in agriculture. Our proof-of-concept study would be an important basis for the further development of field-basis system management.

Dynamics of species-rich predator-prey networks and seasonal alternations of core species

In nature, entangled webs of predator-prey interactions constitute the backbones of ecosystems. Uncovering the network architecture of such trophic interactions has been recognized as the essential step for exploring species with great impacts on ecosystem-level phenomena and functions. However, it has remained a major challenge to reveal how species-rich networks of predator-prey interactions are continually reshaped through time in the wild. Here, we show that dynamics of species-rich predator-prey interactions can be characterized by remarkable network structural changes and alternations of species with greatest impacts on community processes. On the basis of high-throughput detection of prey DNA from 1,556 spider individuals collected in a grassland ecosystem, we reconstructed dynamics of interaction networks involving, in total, 50 spider species and 974 prey species and strains through 8 months. The networks were compartmentalized into modules (groups) of closely interacting predators and prey in each month. Those modules differed in detritus/grazing food chain properties, forming complex fission-fusion dynamics of belowground and aboveground energy channels across the seasons. The substantial shifts of network structure entailed alternations of spider species located at the core positions within the entangled webs of interactions. These results indicate that knowledge of dynamically shifting food webs is crucial for understanding temporally varying roles of 'core species' in ecosystem processes.

Synergistic effects of succession and microtopography of moraine on the fungal spatial diversity in a glacier forefield

Primary succession and microtopography result in environmental changes and are important processes influencing the community assembly of soil fungi in the Arctic region. In glacier forefields that contain a series of moraine ridges, both processes contribute synchronously to fungal spatial diversity. To reveal the synergistic effects of succession and microtopography, we investigated the fungal community structure and environmental variables in the moraines of the Arklio Glacier, Ellesmere Island. The study sites were established at four locations from the top to the bottom of the ridge slope within each of the three moraine ridges of different post-glacial ages. The location-dependent community composition was equally diverse in both the initial and later stages of succession, suggesting that successional time could alter the effects of microtopography on the fungal community. Moreover, our results suggest that fungal communities at different locations follow different successional trajectories, even if they have passed through the same time lapse. Such a synergistic effect of succession and microtopography of moraines does not allow for parallel changes in fungal communities among moraines or among locations, suggesting that the moraine series contributes substantially to fungal spatial diversity in the glacier forefield.

Potential contribution of floral thermogenesis to cold adaptation, distribution pattern, and population structure of thermogenic and non/slightly thermogenic Symplocarpus species

The genus Symplocarpus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of Symplocarpus contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic Symplocarpus renifolius and non/slightly thermogenic Symplocarpus nipponicus. ENM revealed that the distribution of S. nipponicus decreased, whereas that of S. renifolius expanded in the Last Glacial Maximum. Phylogeographic analyses have shown that the population structures of the two species were genetically segmented and that the genetic diversity of S. renifolius was higher than that of S. nipponicus. The phylogenetic relationship between chloroplast and nuclear DNA is topologically different in the two species, which may be due to the asymmetric gene flow ubiquitously observed in plants. The results of this study imply that floral thermogenesis of Symplocarpus contributes to expanding the distribution during an ice age, resulting in increased genetic diversity due to cold adaptation.

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.

Phylogeography of the temperate grassland plant Tephroseris kirilowii (Asteraceae) inferred from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) data

A group of temperate grassland plant species termed the "Mansen elements" occurs in Japan and is widely distributed in the grasslands of continental East Asia. It has been hypothesized that these species are continental grassland relicts in Japan that stretch back to a colder age, but their migration history has not been elucidated. To assess the migration history of the Mansen elements, we performed phylogeographic analyses of Tephroseris kirilowii, a member of this group, using single-nucleotide polymorphisms (SNPs) obtained from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). It was estimated that the Japanese populations of T. kirilowii were divided from those of continental East Asia at 25.2 thousand years ago (ka) with 95% highest probability density interval (HPD) of 15.3-40.0 ka and that Japanese clades first diverged at 20.2 ka with 95% HPD of 10.4-30.1 ka. As the climatically suitable range during the last glacial maximum (LGM) estimated using ecological niche modeling (ENM) was limited in Japan and there was a slight genetic differentiation among Japanese populations, a post-glacial expansion of T. kirilowii in the Japanese Archipelago was indicated.

Environmental influences on microbial community development during organic pinot noir wine production in outdoor and indoor fermentation conditions

The role of microbial diversity in influencing the organoleptic properties of wine and other fermented products is well est ablished, and understanding microbial dynamics within fermentation processes can be critical for quality assurance and product innovation. This is especially true for winemakers using spontaneous fermentation techniques, where environmental factors may play an important role in consistency of product. Here, we use a metabarcoding approach to investigate the influence of two environmental systems used by an organic winemaker to produce wines; vineyard (outdoors) and winery (indoors) to the bacterial and fungal communities throughout the duration of a spontaneous fermentation of the same batch of Pinot Noir grapes. Bacterial (R_ANOSIM = 0.5814, p = 0.0001) and fungal (R_ANOSIM = 0.603, p = 0.0001) diversity differed significantly across the fermentation stages in both systems. Members of the Hyphomicrobium genus were found in winemaking for the first time, as a bacterial genus that can survive alcoholic fermentation. Our results also indicate that Torulaspora delbrueckii and Fructobacillus species might be sensitive to environmental systems. These results clearly reflect the substantial influence that environmental conditions exert on microbial populations at every point in the process of transforming grape juice to wine via fermentation, and offer new insights into the challenges and opportunities for wine production in an ever-changing global climate.

Evaluating the sampling effort for the metabarcoding‐based detection of fish environmental DNA in the open ocean

Clarifying the effect of the sampling protocol on the detection of environmental DNA (eDNA) is essential for appropriately designing biodiversity research. However, technical issues influencing eDNA detection in the open ocean, which consists of water masses with varying environmental conditions, have not been thoroughly investigated. This study evaluated the sampling effort for the metabarcoding‐based detection of fish eDNA using replicate sampling with filters of different pore sizes (0.22 and 0.45 μm) in the subtropical and subarctic northwestern Pacific Ocean and Arctic Chukchi Sea. The asymptotic analysis predicted that the accumulation curves for detected taxa did not saturate in most cases, indicating that our sampling effort (7 or 8 replicates, corresponding to 10.5–40 L of filtration in total) was insufficient to fully assess the species diversity in the open ocean and that tens of replicates or a substantial filtration volume were required. The Jaccard dissimilarities between filtration replicates were comparable with those between the filter types at any site. In subtropical and subarctic sites, turnover dominated the dissimilarity, suggesting that the filter pore size had a negligible effect. In contrast, nestedness dominated the dissimilarity in the Chukchi Sea, implying that the 0.22 μm filter could collect a broader range of eDNA than the 0.45 μm filter. Therefore, the effect of filter selection on the collection of fish eDNA likely varies depending on the region. These findings highlight the highly stochastic nature of fish eDNA collection in the open ocean and the difficulty of standardizing the sampling protocol across various water masses.

Discrepancies of fungi and plants in the pattern of beta-diversity with environmental gradient imply a comprehensive community assembly rule

Beta-diversity partitioning has shown that the nestedness component is developed with environmental stress in a variety of taxa. However, soil fungal community may maintain its turnover components in contrast to the development of plants' nestedness component, and the potential causes remain unclear. To investigate the process of species turnover of soil fungi along a stress gradient in the Arctic, we divided species turnover component into sub-components: βsim_hete and βsim_homo representing species turnover with and without a change in the guilds, respectively. The results indicate that fungal communities maintain their turnover components, unlike plant communities; however, their βsim_hete increased under stressful conditions. Additionally, GDM analysis showed that βsim_hete was mainly explained by stress gradient and plant nestedness, suggesting that the functionality of soil fungi was ecologically filtered by environmental stress and plant community structure. The discordant trend of beta-diversity values between plant and fungi (i.e. development of plant nestedness and maintenance of fungal turnover) is possibly not caused by different assembly rules working in parallel on the two taxa, but according to an ecological rule that reflects plant-fungal interaction.

Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence

Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity.