Highly Variable and Non-complex Diazotroph Communities in Corals From Ambient and High CO2 Environments

The ecological success of corals depends on their association with microalgae and a diverse bacterial assemblage. Ocean acidification (OA), among other stressors, threatens to impair host-microbial metabolic interactions that underlie coral holobiont functioning. Volcanic CO2 seeps offer a unique opportunity to study the effects of OA in natural reef settings and provide insight into the long-term adaptations under a low pH environment. Here we compared nitrogen-fixing bacteria (diazotrophs) associated with four coral species (Pocillopora damicornis, Galaxea fascicularis, Acropora secale, and Porites rus) collected from CO2 seeps at Tutum Bay (Papua New Guinea) with those from a nearby ambient CO2 site using nifH amplicon sequencing to characterize the effects of seawater pH on bacterial communities and nitrogen cycling. Diazotroph communities were of generally low diversity across all coral species and for both sampling sites. Out of a total of 25 identified diazotroph taxa, 14 were associated with P. damicornis, of which 9 were shared across coral species. None of the diazotroph taxa, however, were consistently found across all coral species or across all samples within a species pointing to a high degree of diazotroph community variability. Rather, the majority of sampled colonies were dominated by one or two diazotroph taxa of high relative abundance. Pocillopora damicornis and Galaxea fascicularis that were sampled in both environments showed contrasting community assemblages between sites. In P. damicornis, Gammaproteobacteria and Cyanobacteria were prevalent under ambient pCO2, while a single member of the family Rhodobacteraceae was present at high relative abundance at the high pCO2 site. Conversely, in G. fascicularis diazotroph communities were indifferent between both sites. Diazotroph community changes in response to OA seem thus variable within as well as between host species, potentially arguing for haphazard diazotroph community assembly. This warrants further research into the underlying factors structuring diazotroph community assemblages and their functional role in the coral holobiont.

Comparison of Soil Biological Properties and Bacterial Diversity in Sugarcane, Soybean, Mung Bean and Peanut Intercropping Systems

Sugarcane intercropping with soybean [Glycine max (Linn.) Merr.], mung bean [Vigna radiata (Linn.) Wilczek] and peanut (Arachis hypogaea Linn.) as well as a sugarcane monoculture were conducted to study the impacts of intercropping on soil biological characteristics and bacterial diversity. The results showed that soil cultivable microorganisms, the activities of soil enzymes and microbial biomass carbon, nitrogen, and phosphorus were all significantly improved by intercropping with soybean and mung bean. Additionally, soil bacterial diversity and richness in sugarcane fields were also significantly enhanced by intercropping with soybean and mung bean. In addition, soil bacterial community structures in sugarcane fields can be altered by intercropping with different legumes. Proteobacteria, a high-nutrient-tolerant bacterial assemblage, became the dominant bacteria in the sugarcane-soybean and sugarcane-mung bean intercropped soils. Twenty four, 28, 26 and 27 dominant soil bacterial genera were found after the sugarcane-soybean, sugarcane-mung bean, sugarcane-peanut and sugarcane monoculture treatments, respectively. Sugarcane-mung bean intercropping being the most promising system for regaining and improving soil fertility and soil heath and facilitate agriculture intensification of sugarcane.

Density and de-nitrifying potential of indigenous bacterial assemblage in mangrove and seagrass in the North of Vietnam

This study assessed the density and de-nitrification potential of indigenous microorganisms in mangroves and seagrass beds in northern Vietnam through two mangrove ecosystems in Tien Yen - Quang Ninh and Bang La - Hai Phong and three seagrass beds in Ha Coi and Dam Ha - Quang Ninh and Tam Giang - Thua Thien Hue. The analysis results of 4 sampling times in rainy and dry seasons during 2017–2019 showed that the density of de-nitrifying bacteria ranged from (1.0 × 102)–(4.6 × 103) MPN/mL, averaging 1.1 ± 0.3 × 103 MPN/mL. The density in mangroves was higher than that in seagrass (a = 0.05). De-nitrification rates ranged from 0.0 µgN/wet to 69.0 µgN/wet soil g/hour, averaging 18.4 ± 7.4 µgN/wet soil g/hour. The rate at the experiments added 0.5 mgN/L in seagrass was higher than that in the mangrove. The density and rate of de-nitrification were significantly correlated with many environmental factors, especially density of sulfur-oxidizing bacteria, the density of nitrifying bacteria, pH, Eh, Nts, N-NH4, P- PO4 and BOD5.

Fishing for the Bacteriome of Tropical Tuna

Background : Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their consumption poses a risk of food poisoning through the development of particular bacterial pathogens. However, their microbiome still remains poorly documented. Here, we conducted a multi-compartmental analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. Results : Our results revealed that the composition of the microbiome was independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants were (i) tuna species for the gut and(ii) sampling site for the skin mucus layer, and (iii) a combination of both parameters for the liver. Interestingly, only 4.5% of all ASVs were shared by the three compartments, raising numerous questions about the circulation of microorganisms within the tuna body. Our results also revealed the presence of a unique and diversified bacterial assemblage within the liver, comprising a substantial proportion of histamine-producing bacteria, well known for their potential pathogenicity and their contribution to fish poisoning cases. Conclusions : These results indicate that the tuna liver is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.

Microbiome diversity and host immune functions may define the fate of sponge holobionts under future ocean conditions

The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment, as well as the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the microbiomes and immune repertoire of two sponge species, the demosponge, Neopetrosia compacta and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress. Neopetrosia compacta harbors a diverse bacterial assemblage and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and proteins with immunological domains. Upon exposure to warming and acidification, the microbiome and host transcriptome of N. compacta remained stable, which correlated with high survival. In contrast, the bacterial community of L. chagosensis exhibited drastic restructuring and widespread downregulation of host immune-related pathways, which accompanied tissue necrosis and mortality. Differences in microbiome diversity and immunological repertoire of diverse sponge groups highlight the central role of host-microbe interactions in predicting the fate of sponges under future ocean conditions.

An algal-bacterial symbiotic system of carbon fixation using formate as a carbon source

Algae are an attractive option for CO2 sequestration due to their natural ability to simultaneously fix CO2 and accumulate algal biomass for value-added products. However, the commercial implementation of such technology for efficient capture of CO2 from fossil-derived flue gases is not a reality yet due to several major challenges, such as low gas-liquid mass transport efficiency and relatively high light irradiance demand of algal growth. This study explored an algal-bacterial symbiotic system to utilize formate, a potential intermediate liquid compound of CO2, as carbon source to support microbial growth. The algal-bacterial assemblage, after an adaptive evolution using the formate medium, demonstrated a new route to assimilate CO2 without using high pH cultivations and promote biomass production under low light irradiance condition. The formate based culture system not only resolves CO2 mass transfer limitation, but also expels algae grazers in non-sterilized cultivation conditions. Continuous cultivation of the assemblage on formate led to a carbon capture efficiency of 90% with biomass concentration of 0.92 g/L and biomass productivity of 0.31 g/L/day, which is significantly better than the control cultivation on saturated CO2. In addition, isotope tracing and microbial community analysis offer new insights into formate metabolism and algal-bacterial symbiosis under light and carbon conditions. This study demonstrates a promising route of using electrochemical-derived formate to support algal biorefining.

A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota

Powdery mildew is a foliar disease caused by epiphytically growing obligate biotrophic ascomycete fungi. How powdery mildew colonization affects host resident microbial communities locally and systemically remains poorly explored. We performed powdery mildew (Golovinomyces orontii) infection experiments with Arabidopsis thaliana grown in either natural soil or a gnotobiotic system and studied the influence of pathogen invasion into standing natural multi-kingdom or synthetic bacterial communities (SynComs). We found that after infection of soil-grown plants, G. orontii outcompetes numerous resident leaf-associated fungi. We further detected a significant shift in foliar but not root-associated bacterial communities in this setup. Pre-colonization of germ-free A. thaliana leaves with a bacterial leaf-SynCom, followed by G. orontii invasion, induced an overall similar shift in the foliar bacterial microbiota and minor changes in the root-associated bacterial assemblage. However, a standing root SynCom in root samples remained robust against foliar infection with G. orontii. Although pathogen growth was unaffected by the leaf SynCom, fungal infection caused a more than two-fold increase in leaf bacterial load. Our findings indicate that G. orontii infection affects mainly microbial communities in local plant tissue, possibly driven by pathogen-induced changes in source-sink relationships and host immune status.

Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere

Saponins are the group of plant specialized metabolites which are widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin present in tissues of tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against plant pathogens and herbivores, but its biological function in the rhizosphere remains unknown. Secretion of tomatine was higher at the early growth than the green-fruit stage in hydroponically grown plants, and the concentration of tomatine in the rhizosphere of field-grown plants was higher than that of the bulk soil at all growth stages. The effects of tomatine and its aglycone tomatidine on the bacterial communities in the soil were evaluated in vitro, revealing that both compounds influenced the microbiome in a concentration-dependent manner. Numerous bacterial families were influenced in tomatine/tomatidine-treated soil as well as in the tomato rhizosphere. Sphingomonadaceae species, which are commonly observed and enriched in tomato rhizospheres in the fields, were also enriched in tomatine- and tomatidine-treated soils. Moreover, a jasmonate-responsive ETHYLENE RESPONSE FACTOR 4 mutant associated with low tomatine production caused the root-associated bacterial communities to change with a reduced abundance of Sphingomonadaceae. Taken together, our results highlight the role of tomatine in shaping the bacterial communities of the rhizosphere and suggest additional functions of tomatine in belowground biological communication.

Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance

Bark beetles often serve as forest damaging agents, causing landscape-level mortality. Understanding the biology and ecology of beetles are important for both, gathering knowledge about important forest insects and forest protection. Knowledge about the bark beetle gut-associated bacteria is one of the crucial yet surprisingly neglected areas of research with European tree-killing bark beetles. Hence, in this study, we survey the gut bacteriome from five Ips and one non-Ips bark beetles from Scolytinae. Results reveal 69 core bacterial genera among five Ips beetles that may perform conserved functions within the bark beetle holobiont. The most abundant bacterial genera from different bark beetle gut include Erwinia, Sodalis, Serratia, Tyzzerella, Raoultella, Rahnella, Wolbachia, Spiroplasma, Vibrio, and Pseudoxanthomonas. Notable differences in gut-associated bacterial community richness and diversity among the beetle species are observed. Furthermore, the impact of sampling location on the overall bark beetle gut bacterial community assemblage is also documented, which warrants further investigations. Nevertheless, our data expanded the current knowledge about core gut bacterial communities in Ips bark beetles and their putative function such as cellulose degradation, nitrogen fixation, detoxification of defensive plant compounds, and inhibition of pathogens, which could serve as a basis for further metatranscriptomics and metaproteomics investigations.