Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress.

Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.

Forest carbon stocks increase with higher dominance of ectomycorrhizal trees in high latitude forests.

Understanding the mechanisms controlling forest carbon accumulation is crucial for predicting and mitigating future climate change. Yet, it remains unclear whether the dominance of ectomycorrhizal (EcM) trees influences the carbon accumulation of entire forests. In this study, we analyzed forest inventory data from over 4000 forest plots across Northeast China. We find that EcM tree dominance consistently exerts a positive effect on tree, soil, and forest carbon stocks. Moreover, we observe that these positive effects are more pronounced during unfavorable climate conditions, at lower tree species richness, and during early successional stages. This underscores the potential of increasing the dominance of native EcM tree species not only to enhance carbon stocks but also to bolster resilience against climate change in high-latitude forests. Here we show that forest managers can make informed decisions to optimize carbon accumulation by considering various factors such as mycorrhizal types, climate, successional stages, and species richness.

Single-cell RNA-seq reveals distinct metabolic "microniches" and close host-symbiont interactions in deep-sea chemosynthetic tubeworm.

Vestimentiferan tubeworms that thrive in deep-sea chemosynthetic ecosystems rely on a single species of sulfide-oxidizing gammaproteobacterial endosymbionts housed in a specialized symbiotic organ called trophosome as their primary carbon source. While this simple symbiosis is remarkably productive, the host-symbiont molecular interactions remain unelucidated. Here, we applied an approach for deep-sea in situ single-cell fixation in a cold-seep tubeworm, Paraescarpia echinospica. Single-cell RNA sequencing analysis and further molecular characterizations of both the trophosome and endosymbiont indicate that the tubeworm maintains two distinct metabolic "microniches" in the trophosome by controlling the availability of chemosynthetic gases and metabolites, resulting in oxygenated and hypoxic conditions. The endosymbionts in the oxygenated niche actively conduct autotrophic carbon fixation and are digested for nutrients, while those in the hypoxic niche conduct anaerobic denitrification, which helps the host remove ammonia waste. Our study provides insights into the molecular interactions between animals and their symbiotic microbes.

Biomass ash as soil fertilizers: Supercharging biomass accumulation by shifting auxin distribution.

Growing quantities of biomass ashes (phyto-ashs) are currently produced worldwide due to the increasing biomass consumption in energy applications. Utilization of phyto-ash in agriculture is environmentally friendly solution. However, mechanisms involving the coordination of carbon metabolism and distribution in plants and soil amendment are not well known. In the present study, tobacco plants were chemically-fertilized with or without 2‰ phyto-ash addition. The control had sole chemical fertilizer; for two phyto-ash treatments, the one (T1) received comparable levels of nitrogen, phophorus, and potassium from phyto-ash and fertilizers as the control and another (T2) had 2‰ of phyto-ash and the same rates of fertilizers as the control. Compared with the control, phyto-ash addition improved the soil pH from 5.94 to about 6.35; T2 treatment enhanced soil available potassium by 30% but no difference of other elements was recorded among three treatments. Importantly, bacterial (but not fungal) communities were significantly enriched by phyto-ash addition, with the rank of richness as: T2 > T1 > control. Consistent with amelioration of soil properties, phyto-ash promoted plant growth through enlarged leaf area and photosynthesis and induced outgrowth of lateral roots (LRs). Interestingly, increased auxin content was recorded in 2nd and 3rd leaves and roots under phyto-ash application, also with the rank level as T2 > T1 > control, paralleling with higher transcripts of auxin synthetic genes in the topmost leaf and stronger [3H]IAA activity under phyto-ash addition. Furthermore, exogenous application of analog exogenous auxin (NAA) restored leaf area, photosynthesis and LR outgrowth to the similar level as T2 treatment; conversely, application of auxin transport inhibitor (NPA) under T2 treatment retarded leaf and root development. We demonstrated that phyto-ash addition improved soil properties and thus facilitated carbon balance within plants and biomass accumulation in which shifting auxin distribution plays an important role.

Root biomass and root morphological traits of three shrub species: Implications for the soil anti-scouring resistance of the ecological slope.

The purpose of this study was to determine which shrub species will enhance soil anti-scouring resistance on an ecological slope. Root traits and soil anti-scouring resistance of three shrubs (Amorpha fruticosa Linn (AFL), Swida alba Opiz (SAO) and Lespedeza bicolor Turcz (LBT)) were measured. Results showed that root biomass and root morphological traits of three shrubs were significantly correlated with the soil anti-scouring resistance index. According to the composition characteristic values, root morphological traits among the three shrubs had a high contribution rate. Under two slopes and two rainfall conditions, when root biomass and root morphological traits (e.g., root length, root volume and root surface area) were identical, AFL had the highest soil anti-scouring resistance index. These results suggested that root biomass and morphological traits of AFL had more significant effects on soil anti-scouring resistance comparing with SAO and LBT. Therefore, in engineering practice, AFL with stronger soil anti-scouring resistance can be selected as slope plants.

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment.

BACKGROUND: Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear. RESULTS: The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation. CONCLUSION: This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.

[Main hypotheses on mechanisms underlying plant invasion: A review.] / æ¤ç‰©å ¥ä¾µæœºåˆ¶çš„ä¸»è¦å‡è¯´.

Plant invasion is one of the most serious global problems, destroying ecosystem structure and function. With the severity of plant invasion, it is particularly important to understand the mechanisms of plant invasion in order to control and solve the problem. We summarized different mechanisms of plant invasion and the synergy among them, expounded the allelopathy, the plant-soil feedbacks, the reciprocal symbiosis, the effects of plant functional traits and phenotype plasticity in the process of plant invasion, and comprehensively analyzed the synergy of multiple mechanisms on plant invasion trajectory. According to the results, the invasion trajectory of alien plants in the invasive site was divided into four stages: introduction, colonization, establishment, and invasion. Integrating all kinds of obstacles and promoting factors encountered into it and putting forward the invasion curve of plants would contribute to the future research and management of invasive plants. We further highlighted the current research deficiencies and future research directions and objectives based on analyzing current research methods of plant invasion.

Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences.

Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.

Beneficial effects of warming on temperate tree carbon storage depend on precipitation and mycorrhizal types.

Despite evidence from multiple observation data sets and numerical model simulations that interactions between biotic and abiotic factors control tree carbon (C) storage in the Northern Hemisphere, it remains unclear whether the effect of one factor will be altered by other factors. Here, we used forest inventory data consisting of more than 500,000 trees from 1910 plots to explore the relative importance of these drivers of plant C storage in northeast China. We found that tree C storage was significantly positively associated with mean annual temperature (MAT). After controlling for the role of mean annual precipitation (MAP), directionality in the tree C storage-MAT relationship reversed, indicating that the direction of MAT affecting tree C storage depends on MAP. Accounting for the effects of tree-fungal symbioses on plant resistance to drought and warming, we found that warming increased AM tree C storage even after controlling the role of MAP, but decreased EcM tree C storage after controlling the role of MAP. Our analysis also shows that species richness, especially the relative richness of AM tree species, had a significantly positive relationship with all types of tree C storage. Our findings have implications for improving temperate forest C sink and afforestation strategies: the increasing richness of AM trees has the potential to enhance the tree C sink and reduce the sensitivity of warming-induced tree growth benefits to changes in precipitation.

Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye.

No sunlight can reach the hadal trench, but some fishes dwelling there still have apparent eye morphology. However, whether they are capable of sensing light remains unknown. In this study, the eyes of the dominant hadal endemic snailfish Pseudoliparis swirei from the Mariana Trench were analyzed using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). A total of 2088 proteins were identified in the eye proteome, most of which had at least one hit against public databases and could be mapped to 316 metabolic pathways. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways directly contributing to visual phototransduction were significantly enriched from the top 10% dominant proteins, implying abundant metabolic activities in the eye and it is still a functional visual organ. One rhodopsin was identified in the eye proteome, sequence analysis indicated that it might have an absorption maximum at ∼480 nm and be sensitive to dim blue light. In addition, proteins that might contribute to extreme environment adaptation, such as heat shock proteins and chaperonin-containing T-complex protein 1, were also highly expressed in the eye. Overall, these results provide insights into the molecular mechanism underlying the vision of hadal snailfish and provide a useful database for further research.

In situ bioremediation of Fenton's reaction-treated oil spill site, with a soil inoculum, slow release additives, and methyl-ß-cyclodextrin.

A residential lot impacted by spills from a leaking light heating oil tank was treated with a combination of chemical oxidation and bioremediation to avoid technically challenging excavation. The tank left emptied in the ground was used for slow infiltration of the remediation additives to the low permeability, clayey soil. First, hydrogen peroxide and citrate chelate was added for Fenton's reaction-based chemical oxidation, resulting in a ca. 50% reduction from the initial 25,000 mg/kg average oil concentration in the soil below the tank. Part of this was likely achieved through mobilization of oily soil into the tank, which was beneficial in regards to the following biological treatment. By first adding live bacteria in a soil inoculum, and then oxygen and nutrients in different forms, an approximately 90% average reduction was achieved. To further enhance the effect, methyl-ß-cyclodextrin surfactant (CD) was added, resulting finally in a 98% reduction from the initial average level. The applicability of the surfactant was based on laboratory-scale tests demonstrating that CD promoted oil degradation and, unlike pine soap, was not utilized by the bacteria as a carbon source, and thus inhibiting degradation of oils regardless of the positive effect on biological activity. The effect of CD on water solubility for different hydrocarbon fractions was tested to serve as the basis for risk assessment requirements for authorizing the use of the surfactant at the site.

Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland.

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

Zinc Homeostasis in Bone: Zinc Transporters and Bone Diseases.

Zinc is an essential micronutrient that plays critical roles in numerous physiological processes, including bone homeostasis. The majority of zinc in the human body is stored in bone. Zinc is not only a component of bone but also an essential cofactor of many proteins involved in microstructural stability and bone remodeling. There are two types of membrane zinc transporter proteins identified in mammals: the Zrt- and Irt-like protein (ZIP) family and the zinc transporter (ZnT) family. They regulate the influx and efflux of zinc, accounting for the transport of zinc through cellular and intracellular membranes to maintain zinc homeostasis in the cytoplasm and in intracellular compartments, respectively. Abnormal function of certain zinc transporters is associated with an imbalance of bone homeostasis, which may contribute to human bone diseases. Here, we summarize the regulatory roles of zinc transporters in different cell types and the mechanisms underlying related pathological changes involved in bone diseases. We also present perspectives for further studies on bone homeostasis-regulating zinc transporters.

Insights into the strategy of micro-environmental adaptation: Transcriptomic analysis of two alvinocaridid shrimps at a hydrothermal vent.

Diffusing fluid at a deep-sea hydrothermal vent creates rapid, acute physico-chemical gradients that correlate strongly with the distribution of the vent fauna. Two alvinocaridid shrimps, Alvinocaris longirostris and Shinkaicaris leurokolos occupy distinct microhabitats around these vents and exhibit different thermal preferences. S. leurokolos inhabits the central area closer to the active chimney, while A. longirostris inhabits the peripheral area. In this study, we screened candidate genes that might be involved in niche separation and microhabitat adaptation through comparative transcriptomics. The results showed that among the top 20% of overexpressed genes, gene families related to protein synthesis and structural components were much more abundant in S. leurokolos compared to A. longirostris. Moreover, 15 out of 25 genes involved in cellular carbohydrate metabolism were related to trehalose biosynthesis, versus 1 out of 5 in A. longirostris. Trehalose, a non-reducing disaccharide, is a multifunctional molecule and has been proven to act as a protectant responsible for thermotolerance in Saccharomyces cerevisiae. Putative positively selected genes involved in chitin metabolism and the immune system (lectin, serine protease and antimicrobial peptide) were enriched in S. leurokolos. In particular, one collagen and two serine proteases were found to have experienced strong positive selection. In addition, sulfotransferase-related genes were both overexpressed and positively selected in S. leurokolos. Finally, genes related to structural proteins, immune proteins and protectants were overexpressed or positively selected. These characteristics could represent adaptations of S. leurokolos to its microhabitat, which need to be confirmed by more evidence, such as data from large samples and different development stages of these alvinocaridid shrimps.

The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters.

Alicella gigantea (Alicelloidae) is a scavenger with the largest body size among amphipods. It is a participant in the foodweb of deepsea ecosystem and distributed with vast bathymetric and geographic ranges. In this study, the mitochondrial genome of A. gigantea was completely assembled and characterized. The complete sequence has a total length of 16,851 bp, comprising the usual eukaryotic components, with 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 2 noncoding control regions (CRs). The gene rearrangement and reverse nucleotide strand bias of its mitochondrial genome are similar to those observed in the deepsea amphipod Eurythenes maldoror (Eurytheneidae), but different from the characters of Halice sp. MT-2017 (Dexaminoidea), an inhabitant of a deeper environment. Phylogenetic analysis indicates that A. gigantea occupies the basal branch of deepsea species-E. maldoror and Hirondellea gigas. This phylogeny supports the hypothesis that the evolution of hadal amphipods has undergone a transition from the abyssal depth. Compared to 41 available shallow water equivalents, the four accessible mitochondrial genomes from the deep sea, including the one produced in this study, show significantly fewer charged amino acids in the 13 PCGs, which suggests an adaption to the deepsea environment.

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation.

It is largely unknown how living organisms-especially vertebrates-survive and thrive in the coldness, darkness and high pressures of the hadal zone. Here, we describe the unique morphology and genome of Pseudoliparis swirei-a recently described snailfish species living below a depth of 6,000 m in the Mariana Trench. Unlike closely related shallow sea species, P. swirei has transparent, unpigmented skin and scales, thin and incompletely ossified bones, an inflated stomach and a non-closed skull. Phylogenetic analyses show that P. swirei diverged from a close relative living near the sea surface about 20 million years ago and has abundant genetic diversity. Genomic analyses reveal that: (1) the bone Gla protein (bglap) gene has a frameshift mutation that may cause early termination of cartilage calcification; (2) cell membrane fluidity and transport protein activity in P. swirei may have been enhanced by changes in protein sequences and gene expansion; and (3) the stability of its proteins may have been increased by critical mutations in the trimethylamine N-oxide-synthesizing enzyme and hsp90 chaperone protein. Our results provide insights into the morphological, physiological and molecular evolution of hadal vertebrates.

Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench.

Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.

Nitrogen deposition and decreased precipitation does not change total nitrogen uptake in a temperate forest.

Decreased precipitation and increased anthropogenical by derived nitrogen (N) are important climate change factors that alter the availability of soil water and N which are crucial to root function and morphological traits. However, these factors are seldom explored in forests. To clarify how altered precipitation and N addition affect the uptake of organic and inorganic N by fine roots, a field hydroponic experiment using brief 15N exposures was conducted in a temperate forest in northern China. The root traits related to nutrient foraging (root morphology and mycorrhizal colonization) were measured simultaneously. Our results showed that all three tree species preferred ammonium (NH4+) over glycine and nitrate (NO3-), and NH4+ contributed 73% to the total N uptake from the soil. Uptake of glycine was higher than that of NO3-. Decreased precipitation, N addition, and their interaction increased NH4+ uptake rate compared with the control. Decreased precipitation decreased the glycine and NO3- uptake rate. Moreover, N addition, decreased precipitation and their interaction changed root morphological traits and significantly decreased mycorrhizal colonization. Although our treatments resulted in changes to the root traits and the forms of N uptake by plants, the total amount of N uptake did not change among all treatments. We conclude that although fine root traits of dominant tree species in temperate forests have high plasticity in response to climate change, nutrient balance in plants causes the total amount of N uptake to remain unchanged.

Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish.

Hadal trenches are characterized by not only high hydrostatic pressure but also scarcity of nutrients and high diversity of viruses. Snailfishes, as the dominant vertebrates, play an important role in hadal ecology. Although studies have suggested possible reasons for the tolerance of hadal snailfish to high hydrostatic pressure, little is known about the strategies employed by hadal snailfish to cope with low-nutrient and virus-rich conditions. In this study, the gut microbiota of hadal snailfish was investigated. A novel bacterium named "Candidatus Mycoplasma liparidae" was dominant in the guts of three snailfish individuals from both the Mariana and Yap trenches. A draft genome of "Ca. Mycoplasma liparidae" was successfully assembled with 97.8% completeness by hybrid sequencing. A set of genes encoding riboflavin biosynthesis proteins and a clustered regularly interspaced short palindromic repeats (CRISPR) system was present in the genome of "Ca. Mycoplasma liparidae," which was unusual for Mycoplasma. The functional repertoire of the "Ca. Mycoplasma liparidae" genome is likely set to help the host in riboflavin supplementation and to provide protection against viruses via a super CRISPR system. Remarkably, genes encoding common virulence factors usually exist in Tenericutes pathogens but were lacking in the genome of "Ca. Mycoplasma liparidae." All of these characteristics supported an essential role of "Ca. Mycoplasma liparidae" in snailfish living in the hadal zone. Our findings provide further insights into symbiotic associations in the hadal biosphere.

Toward understanding barnacle cementing by characterization of one cement protein-100kDa in Amphibalanus amphitrite.

Barnacles, as major fouling organisms, have attracted more attentions. It is no doubt that the study on cement proteins is required to illustrate the mechanism of barnacle cementing. A cement protein defined as Aa-cp100k was characterized from Amphibalanus amphitrite in this study. The amino acid sequence of Aa-cp100k was shown a high similarity to other three barnacles including Megabalanus rosa (Mr-cp100k), Tetraclita japonica formosana (Tj-cp100k) and Pollicipes pollicipes (Pp-cp100k). Moreover, the localization of Aa-cp100k in the vacuoles of cyprid ß secretory cells and the adult cement gland cells by immunofluorescence microscopy, indicating that Aa-cp100k existed in both cyprid and adult barnacle. Aa-cp100k from basal plate could be dissolved in urea buffer without high concentration of dithiothreitol (DTT), different from that in Megabalanus rosa, implying diverse possible roles of cp100k in cementing.