Shifts In Community Composition Research Articles

Effects of plant health protecting product applications on the root-associated microbiota of apple saplings and strawberries

The root-associated microbiome has been of keen research interest due to its large potential for increasing plant performance. In agricultural systems, the use of plant health protecting products (PHPP) is essential for obtaining high yields and quality. Knowledge about the impact of PHPP applications on the root-associated microbiome remains limited, especially when applied above ground. We hypothesized that PHPP application leads to specific plant-mediated responses in the rhizosphere microbiota. We applied different PHPPs on greenhouse-grown apple and strawberry plants, cultivated in different soils. The effects of above ground PHPP applications on the root-associated microbiota were analyzed by 16S rRNA gene amplicon sequencing. No consistent effects were observed across three experimental trials, though alpha diversity tended to be decreased after PHPP application. In some cases, shifts in community composition became evident (PERMANOVA R2 = 0.192, p = 0.001) or increases in dispersion (PERMDISP Padj = 0.040). Movento® treatments caused in part deterministic shifts in community assembly, whereas Serenade®ASO treatments caused rather stochastic shifts. Effects were concluded to be probably transient and to disappear without continuous product application. These rather heterogenous temporary responses are in line with the concept of the ‘Anna Karenina Principle’, under which terms PHPP applications can act as mild stress factors and slightly and transiently alter the below ground bacterial community. These findings indicate that above ground PHPP applications can have product specific implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.

Improving restoration outcomes of boreal Sphagnum-dominated peatlands after peat-extraction: The key role of phosphorus fertilization

Fertilization is a common and effective restoration practice for some ecosystems. However, there are still knowledge gaps about the long-term effectiveness and impact of phosphorus fertilization during the restoration of degraded boreal Sphagnum peatlands using the Moss Layer Transfer Technique. Data gathered from 114 peatland sectors restored 1 to 25 years ago, encompassing around 2900 surveyed plots in Eastern Canada, were analyzed to investigate the influence of fertilization on plant re-establishment (cover, height, and aboveground biomass accumulation) and community composition. Fertilization with a low phosphorus dosage (1.64 g P m−2) of granular phosphate rock (P2O5; NPK 0–13-0) proved to accelerate peatland vegetation recovery by favoring a shift in plant community composition towards a Sphagnum dominance. This shift was encouraged by the fast colonization of Polytrichum strictum after fertilization, a nurse plant that stabilizes the peat substrate and facilitates the subsequent establishment of Sphagnum. Phosphorus fertilization increased by 42 % Sphagnum cover 25-year post-restoration and increased approximately by 15 % aboveground biomass accumulation 20-year post-restoration. Conversely, without fertilization, the success of restoration and long-term vegetation trajectories were uncertain. Phosphorus fertilization led to an increase in plant richness in the first 5 to 10 years after restoration and enhanced spatial heterogeneity in species composition throughout the later stages of restoration (20–25 years), suggesting that fertilization may foster dynamic, diverse plant communities. This study emphasizes fertilization's key role in restoring boreal Sphagnum peatland plant communities, especially in areas prone to episodes of freeze-thaw cycles, strongly advocating for the mandatory inclusion of phosphorus fertilization in the restoration process.

Carbon type and quantity regulate soil free-living nitrogen fixation through restructuring diazotrophic community

Free-living nitrogen fixation (FLNF) is a ubiquitous and significant source of new nitrogen in ecosystems. This process requires a substantial amount of energy, and as a result, the input of labile carbon to soils may enhance FLNF. Here, we aim to explore the precise influence of different types and quantities of carbon on FLNF. We conducted experiments where sugars, carboxylic acids, and amino acids (common labile carbon inputs via root exudates) were added to cropland and forest soils. We monitored the changes in FLNF rate and diazotrophic community in response to these additions. Our findings revealed that sugars and carboxylic acids significantly stimulated FLNF rate, with an increase of up to three orders of magnitude, while amino acids either restricted FLNF or had no effect. When a mixture of sugars and carboxylic acids was added, the stimulation of FLNF was not observed until a threshold quantity of carbon was reached, indicating competition between diazotrophs and other microbes. Furthermore, the enhanced FLNF rate following carbon addition was attributable to shifts in diazotrophic community composition (e.g., increased abundance of Paenibacillus, a genus frequently used as biofertilizers), rather than to changes in the overall abundance of diazotrophs (reflected by nifH gene copy number). Our findings highlight the significant role of carbon type and quantity in regulating soil FLNF, partly through restructuring the diazotrophic community. The results have implications for predicting the response of rhizosphere FLNF to shifts in root exudation under environmental changes and can contribute to the application of diazotrophic biofertilizers in sustainable agriculture.

Persistence and Microbiome Modification in Rhizoctonia solani-Inoculated Rhizosphere Following Amendment with a Bacillus Biocontrol Agent

Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered alternatives to chemical pesticides, but their in vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can affect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber and evaluated its impact on bacterial and fungal community composition in the rhizosphere in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude but remained relatively high for the duration of the experiment, in contrast to the root surface, where it was not detected. Amendment with S-25 significantly reduced the incidence of disease caused by R. solani without reducing the relative abundance of the fungal pathogen. Interestingly, R. solani did not substantially alter the rhizosphere microbial community, whereas S-25 reduced bacterial diversity and facilitated a shift in community composition, with increased relative abundance of Acidobacteriota and Actinomycetota, and reduced abundance of Pseudomonadota, Bacteroidota, and Verrucomicrobiota. Collectively, this study provides important insights into the mode of persistence of biocontrol agents and their effect on native microbiomes in the rhizosphere of pathogen-inoculated plants. It demonstrates that amendment can significantly alter local microbiomes and suggests that optimizing amendment regimes or selecting strains with higher rhizosphere competence can enhance future biocontrol agents.

Comparative analysis of bacterial populations in sulfonylurea-sensitive and -resistant weeds: insights into community composition and catabolic gene dynamics

This study aimed to compare the impact of iodosulfuron-methyl-sodium and an iodosulfuron-based herbicidal ionic liquid (HIL) on the microbiomes constituting the epiphytes and endophytes of cornflower (Centaurea cyanus L.). The experiment involved biotypes of cornflower susceptible and resistant to acetolactate synthase inhibition, examining potential bacterial involvement in sulfonylurea herbicide detoxification. We focused on microbial communities present on the surface and in the plant tissues of roots and shoots. The research included the synthesis and physicochemical analysis of a novel HIL, evaluation of shifts in bacterial community composition, analysis of the presence of catabolic genes associated with sulfonylurea herbicide degradation and determination of their abundance in all experimental variants. Overall, for the susceptible biotype, the biodiversity of the root microbiome was higher compared to shoot microbiome; however, both decreased notably after herbicide or HIL applications. The herbicide-resistant biotype showed lower degree of biodiversity changes, but shifts in community composition occurred, particularly in case of HIL treatment.Graphical

Loss of species and functions in a deforested megadiverse tropical forest.

Tropical species richness is threatened by habitat degradation associated with land-use conversion, yet the consequences for functional diversity remain little understood. Progress has been hindered by difficulties in obtaining comprehensive species-level trait information to characterize entire assemblages and insufficient appreciation that increasing land-cover heterogeneity potentially compensates for species loss. We examined the impacts of tropical deforestation associated with land-use heterogeneity on bird species richness, functional redundancy, functional diversity, and associated components (i.e., alpha diversity, species dissimilarity, and interaction strength of the relationship between abundance and functional dissimilarity). We analyzed over 200 georeferenced bird assemblages in the Atlantic Forest of Brazil. We characterized the functional role of the species of each assemblage and modeled biodiversity metrics as a function of forest cover and land-cover heterogeneity. Replacement of native Atlantic Forest with a mosaic of land uses (e.g., agriculture, pastures, and urbanization) reduced bird species richness in a nonrandom way. Core forest species, or species considered sensitive to edges, tended to be absent in communities in heterogenous environments. Overall, functional diversity and functional redundancy of bird species were not affected by forest loss. However, birds in highly heterogenous habitats were functionally distinct from birds in forest, suggesting a shift in community composition toward mosaic-exclusive species led by land-cover heterogeneity. Threatened species of the Atlantic Forest did not seem to tolerate degraded and heterogeneous environments; they remained primarily in areas with large forest tracts. Our results shed light on the complex effects of native forest transformation to mosaics of anthropogenic landscapes and emphasize the importance of considering the effects of deforestation and land-use heterogeneity when assessing deforestation effects on Neotropical biodiversity.

Multidecadal changes in coastal benthic species composition and ecosystem functioning occur independently of temperature-driven community shifts.

Rising global temperatures are often identified as the key driver impacting ecosystems and the services they provide by affecting biodiversity structure and function. A disproportionate amount of our understanding of biodiversity and function is from short-term experimental studies and static values of biodiversity indices, lacking the ability to monitor long-term trends and capture community dynamics. Here, we analyse a biennial dataset spanning 32 years of macroinvertebrate benthic communities and their functional response to increasing temperatures. We monitored changes in species' thermal affinities to examine warming-related shifts by selecting their mid-point global temperature distribution range and linking them to species' traits. We employed a novel weighted metric using Biological Trait Analysis (BTA) to gain better insights into the ecological potential of each species by incorporating species abundance and body size and selecting a subset of traits that represent five ecosystem functions: bioturbation activity, sediment stability, nutrient recycling and higher and lower trophic production. Using biodiversity indices (richness, Simpson's diversity and vulnerability) and functional indices (richness, Rao's Q and redundancy), the community structure showed no significant change over time with a narrow range of variation. However, we show shifts in species composition with warming and increases in the abundance of individuals, which altered ecosystem functioning positively and/or non-linearly. Yet, when higher taxonomic groupings than species were excluded from the analysis, there was only a weak increase in the measured change in community-weighted average thermal affinities, suggesting changes in ecosystem functions over time occur independently of temperature increase-related shifts in community composition. Other environmental factors driving species composition and abundance may be more important in these subtidal macrobenthic communities. This challenges the prevailing emphasis on temperature as the primary driver of ecological response to climate change and emphasises the necessity for a comprehensive understanding of the temporal dynamics of complex systems.

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome?

Soil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil microbiota represent an opportunity to accelerate restoration outcomes. Here, we introduce the concept of ecological phage therapy-the application of phage for the targeted reduction of the most abundant and dominant bacterial taxa present in degraded ecosystems. We propose that naturally occurring bacteriophages-viruses that infect bacteria-could help rapidly shift soil microbiota towards target communities. Bacteriophages sculpt the microbiome by lysis of specific bacteria, and if followed by the addition of reference soil microbiota, such treatments could facilitate rapid reshaping of soil microbiota. Here, we experimentally tested this concept in a pilot study. We collected five replicate pre-treatment degraded soil samples, then three replicate soil samples 48 hours after phage, bacteria, and control treatments. Bacterial 16S rDNA sequencing showed that phage-treated soils had reduced bacterial diversity; however, when we combined ecological phage therapy with reference soil inoculation, we did not see a shift in soil bacterial community composition from degraded soil towards a reference-like community. Our pilot study provides early evidence that ecological phage therapy could help accelerate the reshaping of soil microbiota with the ultimate aim of reducing timeframes for ecosystem recovery. We recommend the next steps for ecological phage therapy be (a) developing appropriate risk assessment and management frameworks, and (b) focussing research effort on its practical application to maximise its accessibility to restoration practitioners.

Long-term warming in a temperate forest accelerates soil organic matter decomposition despite increased plant-derived inputs

Climate change may alter soil microbial communities and soil organic matter (SOM) composition. Soil carbon (C) cycling takes place over multiple time scales; therefore, long-term studies are essential to better understand the factors influencing C storage and help predict responses to climate change. To investigate this further, soils that were heated by 5 °C above ambient soil temperatures for 18 years were collected from the Barre Woods Soil Warming Study at the Harvard Forest Long-term Ecological Research site. This site consists of large 30 × 30 m plots (control or heated) where entire root systems are exposed to sustained warming conditions. Measurements included soil C and nitrogen concentrations, microbial biomass, and SOM chemistry using gas chromatography–mass spectrometry and solid-state 13C nuclear magnetic resonance spectroscopy. These complementary techniques provide a holistic overview of all SOM components and a comprehensive understanding of SOM composition at the molecular-level. Our results showed that soil C concentrations were not significantly altered with warming; however, various molecular-level alterations to SOM chemistry were observed. We found evidence for both enhanced SOM decomposition and increased above-ground plant inputs with long-term warming. We also noted shifts in microbial community composition while microbial biomass remained largely unchanged. These findings suggest that prolonged warming induced increased availability of preferred substrates, leading to shifts in the microbial community and SOM biogeochemistry. The observed increase in gram-positive bacteria indicated changes in substrate availability as gram-positive bacteria are often associated with the decomposition of complex organic matter, while gram-negative bacteria preferentially break down simpler organic compounds altering SOM composition over time. Our results also highlight that additional plant inputs do not effectively offset chronic warming-induced SOM decomposition in temperate forests.

Long-Term Contaminant Exposure Alters Functional Potential and Species Composition of Soil Bacterial Communities in Gulf Coast Prairies.

Environmental pollution is a persistent threat to coastal ecosystems worldwide, adversely affecting soil microbiota. Soil microbial communities perform critical functions in many coastal processes, yet they are increasingly subject to oil and heavy metal pollution. Here, we assessed how small-scale contamination by oil and heavy metal impacts the diversity and functional potential of native soil bacterial communities in the gulf coast prairie dunes of a barrier island in South Texas along the northern Gulf of Mexico. We analyzed the bacterial community structure and their predicted functional profiles according to contaminant history and examined linkages between species diversity and functional potential. Overall, contaminants altered bacterial community compositions without affecting richness, leading to strongly distinct bacterial communities that were accompanied by shifts in functional potential, i.e., changes in predicted metabolic pathways across oiled, metal, and uncontaminated environments. We also observed that exposure to different contaminants can either lead to strengthened or decoupled linkages between species diversity and functional potential. Taken together, these findings indicate that bacterial communities might recover their diversity levels after contaminant exposure, but with consequent shifts in community composition and function. Furthermore, the trajectory of bacterial communities can depend on the nature or type of disturbance.

Responses of soil organic carbon compounds to phosphorus addition between tropical monoculture and multispecies forests

Tropical forests are sensitive to nitrogen (N) and phosphorus (P) availability, and under nutrient application the variation of soil organic carbon (SOC) preserving mechanism remains to be explored. To reveal the forest-specific SOC preservation via biochemical selection in response to nutrient application, we investigated a monoculture (Acacia plantation) and a multispecies forest both with chronic fertilization in subtropical regions, and measured specific fingerprints of plant- and microbial-derived C compounds. In addition, to quantify the effect of P application on SOC content among tropical forests, we conducted a meta-analysis by compiling 125 paired measurements in field experiments from 62 studies. In our field experiment, microbial community composition and activity mediated forest-specific responses of SOC compounds to P addition. The shift of community composition from fungi towards Gram-positive bacteria in the Acacia plantation by P addition led to the consumption of microbial residual C (MRC) as C source; in comparison, P addition increased plant species with less complex lignin substrates and induced microbial acquisition for N sources, thus stimulated the decomposition of both plant- and microbial-derived C. Same with our field experiment, bulk SOC content had neutral response to P addition among tropical forests in the meta-analysis, although divergences could happen among experimental durations and secondary tree species. Close associations among SOC compounds with biotic origins and mineral associated organic C (MAOC) in the multispecies forest suggested contributions of both plant- and microbial-derive C to SOC stability. Regarding that fungal MRC closely associated with MAOC and consisted of soil N pool which tightly coupled to SOC pool, the reduce of fungal MRC by chronic P addition was detrimental to SOC accumulation and stability in tropical forests.

Microeukaryote community coalescence strengthens community stability and elevates diversity.

Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.

Interactions between an arbuscular mycorrhizal inoculum and the root-associated microbiome in shaping the response of Capsicum annuum “Locale di Senise” to different irrigation levels

Abstract Background and aims The use of root-associated microorganisms emerge as a sustainable tool to enhance crop tolerance and productivity under climate change, particularly in drought-affected areas. Here, the impact of an inoculum based on arbuscular mycorrhizal fungi (AMF) was evaluated on pepper (Capsicum annuum L.) cultivation at varying water irrigation treatments (well-watered, reduced irrigation and rain-fed) under open-field conditions. Methods Agronomic and ecophysiological parameters, as well as biochemical analyses on stress markers and phytohormones in leaves and on fruit quality traits, were evaluated, along with the shifts in soil- and root-associated microbial communities. Results Rain-fed water treatment caused reduced fruit sizes, while no differences were detected among well-watered and reduced irrigation. Reduced irrigation did not cause a reduction in stomatal conductance. The highest AM fungal colonization rates were observed under reduced irrigation, and the enhanced flavonoid content and reduced oxidative stress markers in AMF-inoculated plants suggested a synergistic effect of AM fungal inoculation in boosting plant tolerance against stress. A shift in microbial community composition in the different irrigation treatments, associated with different enzymatic activity, highlighted the potential role of microbial dynamics in plant stress response under water-limited conditions. Conclusion The study suggests that a reduced irrigation comes along with beneficial impacts on pepper root associated microbes, while not impairing crop performance and yields, indicating a potential of saving water. All together, our results imply that optimization of irrigation and beneficial plant–microbe interactions, such as AM fungal symbiosis, can improve pepper physiological and productivity features under climate change.

Time is of the essence: A general framework for uncovering temporal structures of communities.

Ecological communities are inherently dynamic: species constantly turn over within years, months, weeks or even days. These temporal shifts in community composition determine essential aspects of species interactions and how energy, nutrients, information, diseases and perturbations 'flow' through systems. Yet, our understanding of community structure has relied heavily on static analyses not designed to capture critical features of this dynamic temporal dimension of communities. Here, we propose a conceptual and methodological framework for quantifying and analysing this temporal dimension. Conceptually, we split the temporal structure into two definitive features, sequence and duration, and review how they are linked to key concepts in ecology. We then outline how we can capture these definitive features using perspectives and tools from temporal graph theory. We demonstrate how we can easily integrate ongoing research on phenology into this framework and highlight what new opportunities arise from this approach to answer fundamental questions in community ecology. As climate change reshuffles ecological communities worldwide, quantifying the temporal organization of communities is imperative to resolve the fundamental processes that shape natural ecosystems and predict how these systems may change in the future.

Elevational shifts in tree community composition in the Brazilian Atlantic Forest related to climate change

AbstractQuestionClimate change induces shifts in species distributions, ultimately changing community composition. Mountains are especially sensitive to climate change, and tree species are predicted to move towards higher elevations, but observed changes are not always unidirectional. The diversity and complexity of tropical and subtropical systems limits our understanding of climate‐induced responses of subtropical mountain forests. Here, we investigated migration trends in tree community composition along an elevational gradient, and between the transition from lowland to montane forests in subtropical forests.LocationBrazilian Atlantic Forest.MethodsWe used thermal affiliations of 627 tree species to calculate community temperature scores (CTS) for different life‐history stages of trees in 96 permanent plots. We compared CTS of different life‐history stages across space and time.ResultsMost tree communities (58%) did not show a significant difference of CTS between life‐history stages, indicating a non‐migration trend. On the other hand, 27% of tree communities showed upward migration and 15% downward migration. Upward migration was more common in montane forests, and downward migration in lowland forests. Our temporal analysis shows significant changes in CTS values for juvenile communities with 0.36°C decrease in lowland forests and 0.34°C increase in montane forests.ConclusionsContrasting results between lowland and montane forest communities indicate that the transition zone influences migration patterns and may reflect differences in species’ thermal limitations, as well as by non‐thermal factors such as biotic interactions. Our findings provide the first evidence of climate change‐induced community shifts in the Brazilian Atlantic Forest. We demonstrated that upward migration trends were predominantly observed in montane–upper mountain forests, while downward migrations were noted in lowland–submontane forests. The thermophilization of montane forests may suggest an increased risk of reduction for cold‐demanding species under climate change scenarios.

Response and recovery of nitrifying moving bed biofilm reactor systems exposed to 1°C with varying levels of ammonia starvation

This study investigated the impact of varying total ammonia nitrogen (TAN) feed levels along with water temperature decreases on the performance of nitrifying moving bed biofilm reactor (MBBR) at 1 °C and its recovery at 3 °C. Five MBBR reactors were operated with different TAN concentrations as water temperature decreased from 20 to 3 °C: reactor R1 at 30 mg N/L, reactor R2 at 20 mg N/L, reactor R3 at 15 mg N/L, reactor R4 at 10 mg N/L and reactor R5 at 0 mg N/L. The corresponding biofilm characteristics were also analyzed to understand further nitrifying MBBR under different TAN feeding scenarios. The findings revealed that the higher TAN levels were before reaching 1 °C, the better nitrification performance and the more biomass grew. However, the highest TAN concentration (30 mg N/L) might negatively affect the nitrification performance, the activity of nitrifiers, and the growth of biofilms at 1 °C because of the toxic effects of un-ionized or free ammonia (FA). It was observed that the activities of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were affected by FA concentrations ranging from 0.2 to 0.7 mg N/L at 1 °C, but they could gradually be adapted to such inhibitory environment, with NOB recovering more quickly and robustly than AOB. The study identified 20 mg N/L (67 % of maximum influent TAN at 1 °C in R2 as the optimal TAN feeding concentration, achieving over 90 % TAN removal and a surface area removal rate (SARR) of 0.78 ± 0.02 g N/m2·d at 1 °C. Meanwhile, R2 also exhibited the highest biofilm mass, with total solids at 13.3 mg/carrier and volatile solids at 11.3 mg/carrier. As TAN was removed, nitrite accumulation was observed at 1 °C, and higher influent TAN concentrations prior to 1 °C appeared to delay the accumulation. When water temperature increased from 1 °C to 3 °C, nitrification performance improved significantly in all reactors without nitrite accumulation, and the higher TAN feeding in the previous stage led to faster recovery. Compared with 20 °C, biofilm became thinner and denser at 1 °C and 3 °C. Furthermore, this study revealed significant shifts in microbial community composition and nitrifier abundances in response to changes in water temperature and influent TAN levels. The dominant nitrifiers were identified as Nitrosomonadaceae (AOB) and Nitrospiraceae (NOB). At 1 °C, the nitrifier abundances were significantly correlated with SARRs, FA, and biofilm density. R2, which exhibited the best nitrification performance, maintained higher nitrifier abundances at 1 °C.

Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence

IntroductionGene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored. ObjectiveThe present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence. MethodsWe collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000 years. We characterized their metagenomes, and identified DNA viruses within these metagenomes. ResultsOur findings reveal a significant shift in viral community composition after 50 years of land reclamation, but soil viral diversity reached a stable phase approximately 300 years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer. ConclusionThese findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.

Weather and leaf age separately contribute to temporal shifts in phyllosphere community structure and composition.

All ITS DNA amplicon sequence raw data are deposited in the NCBI Sequence Read Archive (SRA), BioProject number PRJNA1107252, data will be released upon publication. All community data, metadata, taxonomic data, and R code necessary to reproduce these results are deposited in the GitHub repository archived on Zenodo: 10.5281/zenodo.11106439.

Persistent invasion by non-native species and transition to an upland community after removal of invasive Tamarix in a Californian cienega

The targeted removal of a non-native species can result in secondary invasions and other unexpected shifts in plant community composition, but the persistence of these effects is less well known. We investigated how the plant community changed at three time points including before removal (pre-removal), in the years directly following removal (post-removal), and 16 years following Tamarix removal (recent) in an arid depressional wetland. Non-native species cover increased and several non-native species invaded the study area in the years between post-removal surveys and the recent time period, suggesting Tamarix removal may have been a catalyst for increases in non-native species abundance. We also found an increase in the cover of species tolerating upland conditions, and these species were largely non-native. Overall, interactions between targeted removal and shifts in the abiotic environment due to climate change are important drivers of persistent shifts in the plant community. Hydrogeomorphic restoration is likely needed in tandem with invasive removal to see improvements in riparian health, particularly when the invasive species to be removed is a passenger in addition to being a driver of change.

Saline mine water influences eukaryote life in shallow groundwater of a tropical sandy stream

Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to stable environmental conditions and often have narrow spatial distributions. Traditional methods for characterising these communities, focussing on groundwater-inhabiting macro- and meiofauna (stygofauna), are challenging because of limited taxonomic knowledge and expertise (particularly in less-explored regions), and the time and expense of morphological identification. The primary objective of this study was to evaluate the vulnerability of eukaryote communities in shallow groundwater to mine water discharge containing elevated concentrations of magnesium (Mg) and sulfate (SO4). The study was undertaken in a shallow sand bed aquifer within a wet-dry tropical setting. The aquifer, featuring a saline mine water gradient primarily composed of elevated Mg and SO4, was sampled from piezometers in the creek channel upstream and downstream of the mine water influence during the dry season when only subsurface water flow was present. Groundwater communities were characterised using both morphological assessments of stygofauna from net samples and environmental DNA (eDNA) targeting the 18S rDNA and COI mtDNA genes. eDNA data revealed significant shifts in community composition in response to mine waters, contrasting with findings from traditional morphological composition data. Changes in communities determined using eDNA data were notably associated with concentrations of SO42−, Mg2+ and Na+, and water levels in the piezometers. This underscores the importance of incorporating molecular approaches in impact assessments, as relying solely on traditional stygofauna sampling methods in similar environments may lead to inaccurate conclusions about the responses of the assemblage to studied impacts.