Rhizosphere microbiome dynamics in tropical seagrass under short-term inorganic nitrogen fertilization

Seagrass is an early responder to nitrogen enrichment in oligotrophic oceanic coral atoll environments

Seagrass meadows in oceanic coral atoll settings play key roles in sediment stabilisation and biodiversity enhancement. However, seagrass is susceptible to anthropogenic disturbance including nutrient input. Here, we experimentally enriched Thalassia hemprichii meadows with N-based fertiliser in two similar reef-top settings with different recent histories of disturbance, in Laamu atoll, Maldives. Enrichment resulted in enhanced overall leaf production, but in different ways at the two sites. At the 'more impacted', and slightly deeper site, the dominant effect of high-nutrient treatment was growth of new leaves, but this also coincided with cyanobacteria and filamentous green-algal blooms. In contrast, the 'less impacted' site, leaf extension rates (tagged and new) significantly increased. Isotopic analysis confirmed fertiliser uptake into biomass. Our findings highlight that the response of seagrass to nutrient enrichment is context dependent. This study, the first of its kind in the Indian Ocean, highlights the need and opportunity for nutrient and seagrass monitoring and associated policy development.

Long-term changes in soil biological activity and other properties of raised beds in Longan orchards

Introduction

The Longan fruit tree of the Vietnam Mekong Delta is grown in raised beds to improve water drainage during the rainy season and can live as long as 100 years.

Objective

This research explores the extent to which the soil microorganisms as well as soil physical and chemical properties of these raised beds degrade over a period of 60 years under traditional management practices.

Materials and Methods

Raised bed topsoil samples at depths of 0-20 cm were obtained from four different Longan orchards raised bed age groups: group 1) 15-25 years (L1-L5); group 2) 26-37 years (L6-L10); group 3) 38-45 years (L11-L15); and group 4) 46-60 years. Soil biological properties were tested for nitrogen-fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria, calcium solubilizing bacteria and silicate solubilizing bacteria, β-glucosidase, urease, phosphomonoesterase, and phytase. Soil samples were also tested for moisture content, soil texture, soil porosity, and bulk density as well as soil chemical properties including pH, electrical conductivity (EC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (NH4 +, NO3 -), available phosphorus (AP), exchangeable potassium (K+), exchangeable calcium (Ca2 +), available silicate (SiO2), available copper (Cu), zinc (Zn), boron (B) and manganese (Mn). Key findings: The results showed that soil moisture, soil porosity, sand content, SOM, TP, TK, available P, exchangeable Ca2 +, available Si, nitrogen fixing bacteria number, β-glucosidase, urease, phosphomonoesterase, and phytase gradually and significantly decreased in the raised bed soil as the Longan orchard increased in age. Pearson correlation analysis between the ages of Longan orchards and soil properties revealed that raised bed ages were positively correlated with soil bulk density, but negatively correlated with soil moisture content, soil porosity, SOM, TN, β-glucosidase, urease, phosphomonoesterase, and phytase. Principal component analysis (PCA) showed Longan yields had a positive correlation with available NO3 - but negative correlation with NFB, exchangeable Ca2 +, pH, and available B. These findings reveal that traditional long-term management of Longan trees in raised beds significantly reduce soil organic matter, moisture content, porosity, and soil fertility with impacts on soil microbial numbers and activity within raised bed soils.

Future Directions

This suggests that more sustainable management practices, such as mulch and cover crops that decrease soil compaction and increase soil organic matter, improve soil porosity, total N, and feed soil microorganisms that are critical to nutrient cycling are needed to improve raised bed soil quality.

Host-associated microbes mitigate the negative impacts of aquatic pollution

Pollution can negatively impact aquatic ecosystems, aquaculture operations, and recreational water quality. Many aquatic microbes can sequester or degrade pollutants and have been utilized for bioremediation. While planktonic and benthic microbes are well-studied, host-associated microbes likely play an important role in mitigating the negative impacts of aquatic pollution and represent an unrealized source of microbial potential. For example, aquatic organisms that thrive in highly polluted environments or concentrate pollutants may have microbiomes adapted to these selective pressures. Understanding microbe-pollutant interactions in sensitive and valuable species could help protect human well-being and improve ecosystem resilience. Investigating these interactions using appropriate experimental systems and overcoming methodological challenges will present novel opportunities to protect and improve aquatic systems. In this perspective, we review examples of how microbes could mitigate negative impacts of aquatic pollution, outline target study systems, discuss challenges of advancing this field, and outline implications in the face of global changes.

Microbiomes of Thalassia testudinum throughout the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico are influenced by site and region while maintaining a core microbiome

Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.

Inoculation with plant growth-promoting rhizobacteria improves seagrass Thalassia hemprichii photosynthesis performance and shifts rhizosphere microbiome

Plant growth-promoting rhizobacteria (PGPR) inoculation is a crucial strategy for maintaining the sustainability of agriculture and presents a promising solution for seagrass ecological restoration in the face of disturbances. However, the possible roles and functions of PGPRs in the seagrass rhizosphere remain unclear. Here, we isolated rhizosphere bacterial strains from both reef and coastal regions and screened two PGPR isolates regarding their in vivo functional traits. Subsequently, we conducted microcosm experiments to elucidate how PGPR inoculation affected seagrass photosynthesis and shape within each rhizosphere microbiome. Both screened PGPR strains, Raoultella terrigena NXT28 and Bacillus aryabhattai XT37, excelled at expressing a specific subset of plant-beneficial functions and increased the photosynthetic rates of the seagrass host. PGPR inoculation not only decreased the abundance of sulfur-cycling bacteria, it also improved the abundance of putative iron-cycling bacteria in the seagrass rhizosphere. Strain XT37 successfully colonized the seagrass rhizosphere and displayed a leading role in microbial network structure. As a nitrogen-fixing bacteria, NXT28 showed potential to change the microbial nitrogen cycle with denitrification in the rhizosphere and alter dissimilatory and assimilatory nitrate reduction in bulk sediment. These findings have implications for the development of eco-friendly strategies aimed at exploiting microbial communities to confer sulfide tolerance in coastal seagrass ecosystem.

Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area

Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.

Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model

The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH₄⁺-N and NO₃^--N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes.

Melatonin Attenuates the Urea-Induced Yields Improvement Through Remodeling Transcriptome and Rhizosphere Microbial Community Structure in Soybean

Foliar application of nitrogen to enhance crop productivity has been widely used. Melatonin is an effective regulator in promoting plant growth. However, the effects of melatonin and the combination of melatonin and nitrogen on soybeans yields production remain largely unknown. In this study, a field experiment was conducted to evaluate the effects and mechanisms of spraying leaves with melatonin and urea on soybeans. Foliar application of urea significantly increased soybean yields and melatonin did not affect the yields, while combination of melatonin and urea significantly reduced the yields compared to the application of urea alone. A leaf transcriptional profile was then carried out to reveal the underlying mechanism and found that foliar spraying of urea specifically induced the expression of genes related to amino acid transport and nitrogen metabolism. However, foliar application of melatonin significantly changed the transcriptional pattern established by urea application and increased the expression of genes related to abiotic stress signaling pathways. The effects of melatonin and urea treatment on soil microbiome were also investigated. Neither melatonin nor urea application altered the soil microbial alpha diversity, but melatonin application changed rhizosphere microbial community structure, whereas the combination of melatonin and urea did not. Melatonin or urea application altered the abundance of certain taxa. The number of taxa changed by melatonin treatment was higher than urea treatment. Collectively, our results provide new and valuable insights into the effects of foliar application of melatonin to urea and further show that melatonin exerts strong antagonistic effects on urea-induced soybean yields, gene expression and certain soil microorganisms.

Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution

The global seagrass bed ecosystem acts as a natural ecological barrier in the littoral coastal zone. In recent years, this ecosystem has suffered from serious eutrophication and destruction caused by the continuous expansion of aquaculture. However, our understanding of the influence of aquaculture on the bacterial community remains limited. In this study, we used 16S amplicon sequencing to evaluate the impact of aquaculture feed extract solution on the composition and function of bacterial epiphytes and endophyte communities of the core seagrass from the seagrass bed ecosystem in Hainan, Thalassia hemprichii. The feed extract solution was the main factor that significantly affected the bacterial epiphyte and endophyte community structure of seagrass leaves but had no marked effect on alpha diversity was observed. Additionally, the bacterial epiphyte and endophyte community of the T. hemprichii leaves alleviated the effects of organic matter, sulfide, and nutrients caused by aquaculture wastewater. The feed extract solution promoted the proliferation of Bacteroidales, Vibrio, Desulfobulbaceae, Desulfobacteraceae, Pseudoalteromonas, Paludibacter, Marinomonas, and Pseudomonas in the leaves and root of T. hemprichii, which can effectively improve the digestibility of eutrophication. In fact, Desulfobacteraceae and Desulfobulbaceae can reduce sulfate to sulfide and oxidize sulfide to sulfur within seagrass, indicating that the increase in Desulfobulbaceae and Desulfobacteraceae facilitated the accumulation of sulfide with the treatment of feed extract solution, which may be the reason for the degradation of seagrass caused by aquaculture wastewater containing high concentrations of organic pollutants. These results suggest that although seagrass beds can withstand low concentrations of aquaculture pollutants, sulfide emissions should be minimized.