Polypropylene microfibers negatively affect soybean growth and nitrogen fixation regardless of soil type and mycorrhizae presence.

Recent studies have indicated that soil contamination with microplastics (MPs) can negatively affect agricultural productivity, although these effects vary greatly depending on the context. Furthermore, the mechanisms behind these effects remain largely unknown. In this study, we examined the impact of two concentrations of polypropylene (PP) fibers in the soil (0.4 % and 0.8 % w/w) on soybean growth, nitrogen uptake, biological nitrogen fixation (BNF), and water use efficiency by growing plants in two soil types, with and without arbuscular mycorrhizal fungi (AMF). PP contamination consistently reduced vegetative growth (-12 %, on average compared to the control), with the severity of this effect varying significantly by soil type (more pronounced in Alfisol than in Vertisol). The extent of BNF progressively reduced with the increase in PP contamination level in both soils (on average, -17.1 % in PP0.4 and -27.5 % in PP0.8 compared to the control), which poses clear agro-environmental concerns. Water use efficiency was also reduced due to PP contamination but only in the Alfisol (-9 %, on average). Mycorrhizal symbiosis did not seem to help plants manage the stress caused by PP contamination, although it did lessen the negative impact on BNF. These findings are the first to demonstrate the effect of PP on BNF in soybean plants, underscoring the need to develop strategies to reduce PP pollution in the soil and to mitigate the impact of PP on the functionality and sustainability of agroecosystems.

Geographical, Seasonal, and Growth-Related Dynamics of Gut Microbiota in a Grapevine Pest, Apolygus spinolae (Heteroptera: Miridae).

A number of insects are associated with gut symbiotic microorganisms, wherein symbiotic partners play pivotal metabolic roles for each other such as nutrient supplementation, diet degradation, and pesticide detoxification. Despite the ecological and evolutionary importance of gut microbial communities in insects, their diversity and dynamics remain unclear in many species. The green plant bug Apolygus spinolae, a notorious grapevine pest in Japan, damages grape shoots and severely reduces grape berry yield and quality. The plant bug possesses a simple tubular gut housing ~ 104 bacteria. Here, we investigated geographic, seasonal, and growth-related dynamics of gut microbiota by high-throughput sequencing in 82 individuals (11 nymphs and 71 adults) from five locations in Hokkaido, Japan. In plant bugs, gut microbiota changed dynamically depending on region, season, and developmental stage. Among the gut bacteria, Serratia was consistently and abundantly detected and was significantly affected by seasonal changes. In addition, Caballeronia, known as a specific symbiont in some stinkbug species, was abundantly detected, especially in insects collected in late summer despite A. spinolae complete lack of midgut crypts known as symbiotic organ harboring Caballeronia in other stinkbug species. Considering their prevalence among host bug populations, it is possible these gut microorganisms play a pivotal role in the adaptation of the green plant bug to grapevine fields, although further confirmation through rearing experiments is needed.

Description and Phylogenetic Position of a New Genus and Species of Deep-Water Alpheid Shrimp Associated with Glass Sponges off New Caledonia (Decapoda: Caridea).

Batellopsis paula gen. et sp. nov., a new hexactinellid-associated alpheid shrimp, is described based on a single specimen collected at a depth of 477-503 m north of Île des Pins, New Caledonia. Batellopsis gen. nov. is part of a clade of four genera all containing hexactinellid-associated species, for which a molecular phylogeny is presented. The evolution of several morphological characters, including orbital teeth, a bulgefossa system on the fingers of the first pereiopod chela, and groups of microserrulate setae on the second pereiopod chela, is discussed in light of phylogenetic results.

Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis.

Rhizobium etli CFN42 proteome-transcriptome mixed data of exponential growth and nitrogen-fixing bacteroids, as well as Sinorhizobium meliloti 1021 transcriptome data of growth and nitrogen-fixing bacteroids, were integrated into transcriptional regulatory networks (TRNs). The one-step construction network consisted of a matrix-clustering analysis of matrices of the gene profile and all matrices of the transcription factors (TFs) of their genome. The networks were constructed with the prediction of regulatory network application of the RhizoBindingSites database (http://rhizobindingsites.ccg.unam.mx/). The deduced free-living Rhizobium etli network contained 1,146 genes, including 380 TFs and 12 sigma factors. In addition, the bacteroid R. etli CFN42 network contained 884 genes, where 364 were TFs, and 12 were sigma factors, whereas the deduced free-living Sinorhizobium meliloti 1021 network contained 643 genes, where 259 were TFs and seven were sigma factors, and the bacteroid Sinorhizobium meliloti 1021 network contained 357 genes, where 210 were TFs and six were sigma factors. The similarity of these deduced condition-dependent networks and the biological E. coli and B. subtilis independent condition networks segregates from the random Erdös-Rényi networks. Deduced networks showed a low average clustering coefficient. They were not scale-free, showing a gradually diminishing hierarchy of TFs in contrast to the hierarchy role of the sigma factor rpoD in the E. coli K12 network. For rhizobia networks, partitioning the genome in the chromosome, chromids, and plasmids, where essential genes are distributed, and the symbiotic ability that is mostly coded in plasmids, may alter the structure of these deduced condition-dependent networks. It provides potential TF gen-target relationship data for constructing regulons, which are the basic units of a TRN.

Symbiosis between the Javan rhinoceros and slender-billed crow: A novel inferred cleaning mutualism.

Over the past century, the Javan rhinoceroses' (Rhinoceros sondaicus) secluded nature and low population size have led to a gap in knowledge of their ecology. With fewer than 80 individuals surviving in a single population in West Java, Indonesia, the Javan rhinoceros is one of the most critically endangered mammals in the world. As part of a pilot bioacoustics study of the Javan rhinoceros in 2019, we systematically reviewed camera trap footage from the core Javan rhinoceros range in Ujung Kulon National Park (UKNP). In doing so, we discovered a previously unknown interaction between the Javan rhinoceros and the slender-billed crow (Corvus enca), in which the crow finds and eats ectoparasites from the rhinoceros (Figure 1). We describe this interaction and suggest that it may represent a cleaning mutualism with benefits for both the crow and the rhinoceros.

Boosting K+-ionic Conductivity of Layered Oxides via Regulating P2/P3 Heterogeneity and Reciprocity for Room-temperature Quasi-solid-state Potassium Metal Batteries.

Solid-state potassium metal batteries are promising candidates for grid-scale energy storage due to their low cost, high energy density and inherent safety. However, solid state K-ion conductors struggle with poor ionic conductivity due to the large ionic radius of K+-ions. Herein, we report precise regulation of phase heterogeneity and reciprocity of the P2/P3-symbiosis K0.62Mg0.54Sb0.46O2 solid electrolyte (SE) for boosting a high ionic conductivity of 1.6×10-4 S cm-1 at 25 °C. The bulk ionic conducting mechanism is explored by elucidating the effect of atomic stacking mode within the layered framework on K+-ion migration barriers. For ion diffusion at grain boundaries, the P2/P3 biphasic symbiosis property assists in tunning the SE microstructure, which crystallizes in rod-like particles with lengths of tens of micrometers facilitating long-distance ion transport and significantly decreasing grain boundary resistance. Potassium metal symmetric cells using the modified SE deliver excellent cycling life over 300 h at 0.1 mA cm-2 and a high critical current density of 0.68 mA cm-2. The quasi-solid-state potassium metal batteries (QSSKBs) coupled with two kinds of layered oxide cathodes demonstrate remarkable stability over 300 cycles, outperforming the liquid electrolyte counterparts. The QSSKB system provides a promising strategy for high-efficiency, safe, and durable large-scale energy storage.

Rapid loss of nutritional symbionts in an endemic Hawaiian herbivore radiation is associated with plant galling habit.

Insect herbivores frequently co-speciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host plant species, Metrosideros polymorpha within the last ∼5MY. Using 16S rRNA sequencing we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few MY, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, lysine) as well as B-vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.

Characteristics and functions of volatile organic compounds in the tripartite symbiotic system of Gastrodia elata-Armillaria gallica-Rahnella aceris HPDA25.

Tripartite interactions among plants, fungi, and bacteria are critical for maintaining plant growth and fitness, and volatile organic compounds (VOCs) play a significant role in these interactions. However, the functions of VOCs within the niche of mycoheterotrophic plants, which represent unique types of interactions, remain poorly understood. Gastrodia elata, a mycoheterotrophic orchid species, forms a symbiotic relationship with specific Armillaria species, serving as a model system to investigate this intriguing issue. Rahnella aceris HPDA25 is a plant growth-promoting bacteria isolated from G. elata, which has been found to facilitate the establishment of G. elata-Armillaria symbiosis. In this study, using the tripartite symbiotic system of G. elata-Armillaria gallica-R. aceris HPDA25, we investigate the role of VOCs in the interaction among mycoheterotrophic plants, fungi, and bacteria. Our results showed that 33 VOCs of HPDA25-inducible symbiotic G. elata elevated compared to non-symbiotic G. elata, indicating that VOCs indeed play a role in the symbiotic process. Among these, 21 VOCs were accessible, and six active VOCs showed complete growth inhibition activities against A. gallica, while R. aceris HPDA25 had no significant effect. In addition, three key genes of G. elata have been identified that may contribute to the increased concentration of six active VOCs. These results revealed for the first time the VOCs profile of G. elata and demonstrated its regulatory role in the tripartite symbiotic system involving G. elata, Armillaria, and bacteria.

Nature of back slopping kombucha fermentation process: insights from the microbial succession, metabolites composition changes and their correlations.

Kombucha, a fermented tea prepared with a symbiotic culture of bacteria and yeast (SCOBY), offers a unique and unpredictable home-brewed fermentation process. Therefore, the need for a controlled kombucha fermentation process has become evident, which requiring a thorough understanding of the microbial composition and its relationship with the metabolites produced. In this study, we investigated the dynamics of microbial communities and metabolites over a 12-day fermentation period of a conventional kombucha-making process. Our findings revealed similarities between the microbial communities in the early (0-2 days) and late (10-12 days) fermentation periods, supporting the principle of back-slopping fermentation. Untargeted metabolite analysis unveiled the presence of harmful biogenic amines in the produced kombucha, with concentrations increasing progressively throughout fermentation, albeit showing relatively lower abundance on days 8 and 12. Additionally, a contrasting trend between ethanol and caffeine content was observed. Canonical correspondence analysis highlighted strong positive correlations between specific bacterial/yeast strains and identified metabolites. In conclusion, our study sheds light on the microbial and metabolite dynamics of kombucha fermentation, emphasizing the importance of microbial control and quality assurance measures in the production process.

Phenoxyacetic acid enhances nodulation symbiosis during the rapid growth stage of soybean.

Root exudates are known signaling agents that influence legume root nodulation, but the molecular mechanisms for nonflavonoid molecules remain largely unexplored. The number of soybean root nodules during the initial growth phase shows substantial discrepancies at distinct developmental junctures. Using a combination of metabolomics analyses on root exudates and nodulation experiments, we identify a pivotal role for certain root exudates during the rapid growth phase in promoting nodulation. Phenoxyacetic acid (POA) was found to activate the expression of GmGA2ox10 and thereby facilitate rhizobial infection and the formation of infection threads. Furthermore, POA exerts regulatory control on the miR172c-NNC1 module to foster nodule primordia development and consequently increase nodule numbers. These findings collectively highlight the important role of POA in enhancing nodulation during the accelerated growth phase of soybeans.

Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests.

Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.

The Role of Mycorrhizal Fungi in Orchids Mycobiont and Orchids.

BACKGROUND: In nature, orchid plants are obligate myco-heterotrophs, and rely on mycorrhizal nutrient resources to grow and sustain in the wild, until they become physiologically active photosynthetic plants. Their seeds lack nutrient reserves and receive the necessary carbon from symbiotic fungi during germination. A mycorrhizal fungus provides nutrients, especially sugars, as well as water to the corresponding host plant. The range and distribution of orchid mycorrhizal fungi influence the survivability of orchid populations in their natural habitats. Mycorrhizae form symbiotic connections with the parenchymatous tissues of the roots of orchid plants. OBJECTIVE: The objective of this study was to examine the presence of mycorrhiza in the roots of Aerides multiflora during the vegetative phase Methods: Fresh roots were hand-sectioned, and thin sections were observed under the microscope to locate the presence of mycorrhiza. Simultaneously, to observe the expansion of mycorrhiza in the cortical region. RESULTS: During the vegetative phase of plant growth, a peloton-like structure forms within the cortical region of the orchid roots. Mycorrhizae was observed to be distributed throughout the cortical layer of the root. CONCLUSION: This communication reviews the role of mycorrhiza in orchid plants.

HcZnT2 is a highly mycorrhiza-induced zinc transporter from Hebeloma cylindrosporum in association with pine.

Zinc (Zn) shortage is a common micronutrient deficiency affecting plants worldwide, while Zn toxicity may occur when this metal is in excess. Ectomycorrhizal (ECM) fungi are known to be able to modulate the transfer of macro- and microelements, among them Zn, to the plant. However, the underlying mechanisms are not well understood. We identified the HcZnT2 gene from the ECM fungus Hebeloma cylindrosporum, encoding a member of the Cation Diffusion Facilitator (CDF) family including Zn transporters, and analyzed its transcriptional regulation, the transport function by yeast complementation experiments, and its subcellular localization using a GFP fusion protein in yeast. HcZnT2 is highly induced during mycorrhization of Pinus pinaster, and upregulated in presence of the host plant root even without any direct contact. However, HcZnT2 is repressed by Zn excess conditions. By functional expression in yeast, our results strongly support the ability of HcZnT2 to transport Zn and, to a lesser extent, manganese. HcZnT2 localization was associated with the endoplasmic reticulum of yeast. Mycorrhizal gene activation at low external Zn suggests that the Zn transporter HcZnT2 might be important for the early establishment of the ECM symbiosis during Zn deficiency, rather than under Zn excess. HcZnT2 arises as an extremely remarkable candidate playing a key role in Zn homeostasis and regulation in ectomycorrhiza.

A mechanistic framework for complex microbe-host symbioses.

Virtually all multicellular organisms on Earth live in symbiotic associations with complex microbial communities: the microbiome. This ancient relationship is of fundamental importance for both the host and the microbiome. Recently, the analyses of numerous microbiomes have revealed an incredible diversity and complexity of symbionts, with different mechanisms identified as potential drivers of this diversity. However, the interplay of ecological and evolutionary forces generating these complex associations is still poorly understood. Here we explore and summarise the suite of ecological and evolutionary mechanisms identified as relevant to different aspects of microbiome complexity and diversity. We argue that microbiome assembly is a dynamic product of ecology and evolution at various spatio-temporal scales. We propose a theoretical framework to classify mechanisms and build mechanistic host-microbiome models to link them to empirical patterns. We develop a cohesive foundation for the theoretical understanding of the combined effects of ecology and evolution on the assembly of complex symbioses.

Two +ssRNA mycoviruses cohabiting the fungal cultivar of leafcutter ants.

Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.

The co-dispersal strategy of Endocarpon (Verrucariaceae) shapes an unusual lichen population structure.

The reproduction and dispersal strategies of lichens play a major role in shaping their population structure and photobiont diversity. Sexual reproduction, which is common, leads to high lichen genetic diversity and low photobiont selectivity. However, the lichen genus Endocarpon adopts a special co-dispersal model in which algal cells from the photobiont and ascospores from the mycobiont are released together into the environment. To explore the dispersal strategy impact on population structures, a total of 62 Endocarpon individuals and 12 related Verrucariaceae genera individuals, representing co-dispersal strategy and conventional independent dispersal mode were studied. Phylogenetic analysis revealed that Endocarpon, with a large-scale geographical distribution, showed an extremely high specificity of symbiotic associations with their photobiont. Furthermore, three types of group I intron at 1769 site have been found in most Endocarpon mycobionts, which showed a high variety of group I intron in the same insertion site even in the same species collected from one location. This study suggested that the ascospore-alga co-dispersal mode of Endocarpon resulted in this unusual mycobiont-photobiont relationship; also provided an evidence for the horizontal transfer of group I intron that may suggest the origin of the complexity and diversity of lichen symbiotic associations.

Gene expression plasticity governing symbiosis during natural coral bleaching.

The increasing global frequency and severity of coral bleaching events, driven by the loss of endosymbiotic algae, pose a significant threat to these vital ecosystems. However, gene expression plasticity offers a potential mechanism for rapid and effective acclimatization to environmental changes. We employed dual transcriptomics to examine the gene expression profile of Seriatopora hystrix, an ecologically important scleractinian coral, across healthy, mildly bleached, and severely bleached colonies collected from the waters of Likupang, North Sulawesi, Indonesia. Our analysis revealed that coral bleaching is associated with gene plasticity in calcium signaling and focal adhesion within coral hosts, as well as with endoplasmic reticulum stress in symbionts. Notably, we identified specific genes associated with innate immunity that were predominantly overexpressed in mildly bleached coral hosts. This overexpression implies that high expression plasticity of these key genes might contribute to bleaching resistance and the preservation of the host-symbiont relationship. Our findings offer a detailed insight into the dynamics of bleaching resistance in S. hystrix, shedding light on the variability of bleaching risks in Indonesian reefs and underscoring the coral's ability to utilize gene expression plasticity for immediate survival and potential long-term adaptation to climate changes.

Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.

BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages. RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages. CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

Identification and functional analysis of recent IS transposition events in rhizobia.

Rhizobia are alpha- and beta- Proteobacteria that, through the establishment of symbiotic interactions with leguminous plants, are able to fix atmospheric nitrogen as ammonium. The successful establishment of a symbiotic interaction is highly dependent on the availability of nitrogen sources in the soil, and on the specific rhizobia strain. Insertion sequences (ISs) are simple transposable genetic elements that can move to different locations within the host genome and are known to play an important evolutionary role, contributing to genome plasticity by acting as recombination hot-spots, and disrupting coding and regulatory sequences. Disruption of coding sequences may have occurred either in a common ancestor of the species or more recently. By means of ISComapare, we identified Differentially Located ISs (DLISs) in nearly related rhizobial strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium. Our results revealed that recent IS transposition could have a role in adaptation by enabling the activation and inactivation of genes that could dynamically affect the competition and survival of rhizobia in the rhizosphere.

Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.

Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.