Community Shifts Research Articles

Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities.

Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate-a potential virulence factor of R. solani-while simultaneously possessing the ability to metabolize keratin.

Extinction drives recent thermophilization but does not trigger homogenization in forest understorey.

The ongoing climate change is triggering plant community thermophilization. This selection process ought to shift community composition towards species adapted to warmer climates but may also lead to biotic homogenization. The link between thermophilization and homogenization and the community dynamics that drive them (colonization and extinction) remain unknown but is critical for understanding community responses under rapid environmental change. We used 14,167 pairs of plots to study shifts in plant community during 10 years of rising temperature in 80 forest ecoregions of France. We computed community mean thermal optimum (thermophilization) and Δβ-diversity (homogenization) for each ecoregion and partitioned these changes into extinction and colonization dynamics of cold- and warm-adapted species. Forest understorey communities thermophilized on average by 0.12 °C per decade and up to 0.20 °C per decade in warm ecoregions. This rate was entirely driven by extinction dynamics. Extinction of cold-adapted species was a driver of homogenization but it was compensated for by the colonization of rare species and the extinction of common species, resulting in the absence of an apparent homogenization trend. Here we show a dieback of present cold-adapted species rather than an adaptation of communities via the arrival of warm-adapted species, with a mutually cancelling effect on β-diversity. These results suggest that a future loss of biodiversity and delayed biotic homogenization should be considered.

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach.

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.

Remediation of soda-saline-alkali soil through soil amendments: Microbially mediated carbon and nitrogen cycles and remediation mechanisms

Due to the high salt content and pH value, the structure of saline-sodic soil was deteriorated, resulting in decreased soil fertility and inhibited soil element cycling. This, in turn, caused significant negative impacts on crop growth, posing a major challenge to global agriculture and food security. Despite numerous studies aimed at reducing the loss of plant productivity in saline-sodic soils, the knowledge regarding shifts in soil microbial communities and carbon/nitrogen cycling during saline-sodic soil improvement remains incomplete. Consequently, we developed a composite soil amendment to explore its potential to alleviate salt stress and enhance soil quality. Our findings demonstrated that the application of this composite soil amendment effectively enhanced microbial salinity resistance, promotes soil carbon fixation and nitrogen cycling, thereby reducing HCO3− concentration and greenhouse gas emissions while improving physicochemical properties and enzyme activity in the soil. Additionally, the presence of CaSO4 contributed to a decrease in water-soluble Na+ content, resulting in reduced soil ESP and pH by 14.64 % and 7.42, respectively. Our research presents an innovative approach to rehabilitate saline-sodic soil and promote ecological restoration through the perspective of elements cycles.

Microbial mediation of soil carbon loss at the potential climax of alpine grassland under warming

Soil in high latitude and altitude cold regions contains over half of soil organic carbon (SOC) globally, so the decomposition of these SOCs under climate warming could release huge amounts of carbon dioxide to the atmosphere, amplifying climate warming. However, it is still unclear how the SOC storages will change when the ecosystem reaches the final and stable stage (i.e., the climax) under long-term warming. This is mainly because the turnover times of SOC in cold regions exceeds hundreds or even thousands of years, much longer than the periods of simulated warming experiments. Herein we used natural geothermal warming gradients in a Tibetan alpine grassland to determine SOC changes and underlying plant and microbial mechanisms at the potential climax. SOC concentrations were significantly decreased by 21.4%–30.6% under high-level soil warming (+4∼+6 °C), but remained unchanged under low-level soil warming (+2 °C). The losses of SOC were primarily from mineral-associated organic carbon, rather than unprotected particulate organic carbon. The shifts of microbial communities and associated decline of microbial carbon use efficiency, rather than plant-driven carbon fluxes, substantially contributed to the SOC changes. This observed SOC losses at the climax of alpine grassland by high-level warming provide strong empirical support for the positive soil carbon-climate feedback in cold regions, which could not be concluded from short-term experiments or only based on ecosystem carbon fluxes alone. The divergent responses of SOC to different degrees of warming suggest that models must account for these heterogeneous carbon dynamics for projecting future climate warming scenarios.

Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts

AbstractEnvironmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA‐based species detection in streams and rivers may be influenced by sampling season and other key factors such as water temperature and discharge. Research linking these factors and also informing on the potential of eDNA metabarcoding to detect shifts in ecological signatures, such as species phenology and functional feeding groups across seasons, is missing. To address this gap, we collected water samples every 2 weeks for 15 months at a long‐term ecological research (LTER) site and at three different positions in the river's cross section, specifically the water surface, riverbed, and riverbank. For these 102 samples, we analyzed macroinvertebrate species and molecular operational taxonomic unit (OTU) richness and temporal community turnover across seasons based on cytochrome c oxidase subunit I (COI) metabarcoding data. Using Generalized Additive Models, we found a significant influence of sampling season on species richness. Community turnover followed a cyclic pattern, reflecting the continuous change of the macroinvertebrate community throughout the year (“seasonal clock”). Although water temperature had no influence on the inferred species richness, higher discharge reduced the number of Annelida and Ephemeroptera species detectable with eDNA. Most macroinvertebrate taxa showed the highest species richness in spring, in particular merolimnic species with univoltine life cycles. Further, we detected an increase in the proportion of shredders in winter and parasites in summer. Our results show the usefulness of highly resolved eDNA metabarcoding time series data for ecological research and biodiversity monitoring in streams and rivers.

Anaerobic digestion of wastewater from hydrothermal liquefaction of sewage sludge and combined wheat straw-manure

Hydrothermal liquefaction (HTL) shows promise for converting wet biomass waste into biofuel, but the resulting high-strength process water (PW) requires treatment. This study explored enhancing energy recovery by anaerobic digestion using semi-batch reactors. Co-digesting manure with HTL-PW from wheat straw-manure co-HTL yielded methane (43–49% of the chemical oxygen demand, COD) at concentrations up to 17.8 gCOD·L-1, whereas HTL-PW from sewage sludge yielded methane (43% of the COD) up to only 12.8 gCOD·L-1 and complete inhibition occurred at 17 gCOD·L-1. Microbial community shifts confirmed inhibition of methanogenic archaea, while hydrolytic-fermentative bacteria were resilient. Differences in chemical composition, particularly higher levels of N-containing heterocyclic compounds in PW of sewage sludge, likely caused the microbial inhibition. The considerable potential of combining HTL with anaerobic digestion for enhanced energy recovery from straw-manure in an agricultural context is demonstrated, yet sewage sludge HTL-PW requires more advanced approaches to deal with methanogenesis inhibitors.

A modified Mediterranean-style diet enhances brain function via specific gut-microbiome-brain mechanisms.

Alzheimer's disease (AD) is a debilitating brain disorder with rapidly mounting prevalence worldwide, yet no proven AD cure has been discovered. Using a multi-omics approach in a transgenic AD mouse model, the current study demonstrated the efficacy of a modified Mediterranean-ketogenic diet (MkD) on AD-related neurocognitive pathophysiology and underlying mechanisms related to the gut-microbiome-brain axis. The findings revealed that MkD induces profound shifts in the gut microbiome community and microbial metabolites. Most notably, MkD promoted growth of the Lactobacillus population, resulting in increased bacteria-derived lactate production. We discovered elevated levels of microbiome- and diet-derived metabolites in the serum as well, signaling their influence on the brain. Importantly, these changes in serum metabolites upregulated specific receptors that have neuroprotective effects and induced alternations in neuroinflammatory-associated pathway profiles in hippocampus. Additionally, these metabolites displayed strong favorable co-regulation relationship with gut-brain integrity and inflammatory markers, as well as neurobehavioral outcomes. The findings underscore the ameliorative effects of MkD on AD-related neurological function and the underlying gut-brain communication via modulation of the gut microbiome-metabolome arrays.

Environmental DNA identifies coastal plant community shift 1,000 years ago in Torrens Island, South Australia

Anthropogenic activities are causing detrimental changes to coastal plants– namely seagrass, mangrove, and tidal marshes. Looking beyond recent times to past vegetation dynamics is critical to assess the response and resilience of an environment to change. Here, we develop a high-resolution multi-proxy approach, providing a new evidence base to decipher long-term change in coastal plant communities. Combining targeted environmental DNA analysis with chemical analysis of soils, we reconstructed 4,000 years of change at a temperate wetland on Torrens Island South Australia and identified an ecosystem shift that occurred ~ 1000 years ago. What was once a subtidal seagrass system shifted to an intertidal mangrove environment that persists at this site today. We demonstrate that high-resolution historical changes in coastal vegetation can be attained using these proxies. This approach could be applied to other ecosystems to improve the way we protect, conserve, and restore vegetated ecosystems.

Liver cirrhosis and antibiotic therapy but not TIPS application leads to a shift of the intestinal bacterial communities: A controlled, prospective study.

The gut-liver axis is discussed to play an important role in hepatic cirrhosis. Decompensated liver cirrhosis is associated with portal hypertension, which can lead to a variety of complications. Transjugular intrahepatic portosystemic shunt (TIPS) is an established treatment option for the complications of portal hypertension. In this study we focused on the effect of TIPS on intestinal microbial composition in cirrhotic patients. Thirty patients with liver cirrhosis were compared to 18 healthy adults. Seventeen patients with cirrhosis and portal hypertension received a TIPS. Clinical characteristics, including age, sex, and liver function measured with a Child-Pugh score and model for end-stage liver disease score, were obtained. Intestinal microbial composition was assessed via 16S rRNA gene amplicon sequencing from stool probes before and after TIPS. TIPS led to a reduction of hepatic venous pressure gradient. However, TIPS did not cause a shift in the intestinal bacterial communities. Independent from the application of TIPS, antibiotic therapy was associated with a significant difference in the intestinal bacterial microbiota and also a reduced α-diversity. In addition, a significant difference was observed in the intestinal bacterial composition between patients with liver cirrhosis and healthy controls. The presence of liver cirrhosis and the use of antibiotic therapy, but not the application of TIPS, were associated with a significant shift of the intestinal bacterial communities, showing a high impact on the microbiota of patients with liver cirrhosis.

Spatial and Temporal Variability in Water Quality and Phytoplankton Community Composition in Charleston Harbor

The Charleston Harbor estuary is a dynamic ecosystem draining three rivers that surround the rapidly urbanizing greater Charleston area. Projected climate change impacts include elevated sea surface temperature and local changes in water quality that will likely alter biogeochemical cycling as well as phytoplankton abundance and community composition. Partnering with the local non-profit organization Charleston Waterkeeper, surface water samples were collected from late April through October 2021 at 20 sites in the Charleston Harbor estuary system. Water quality parameters measured included sea surface temperature (SST), salinity, pH, dissolved inorganic carbon, chromophoric dissolved organic matter (CDOM), phytoplankton pigments and nitrate and phosphate concentrations. Relatively high (6—16 μM) nitrate values were observed throughout the year and the nitrate to phosphate (N:P) ratios were consistently elevated (50—200) relative to the Redfield ratio of 16. Analysis of variance indicated that the delivery of nitrate, phosphate, and CDOM into the estuary came from upriver of the Charleston Harbor. For instance, CDOM was significantly impacted by tidal stage (p < 0.05) and was negatively correlated with salinity at low salinity sites, but no correlation was observed at high salinity sites. Seasonal patterns in phytoplankton community abundance and composition were driven by changes in SST, as overall phytoplankton biomass increased with a community shift from diatoms during colder months to flagellated cells such as prasinophytes during the warmer summer months. Phytoplankton diversity was greatest during the early summer and lowest in October. This study provides a reference baseline for water quality parameters and phytoplankton community composition in an estuarine ecosystem that is changing rapidly due to dredging and climate change processes.

Neuromorphic Camera Denoising Using Graph Neural Network-Driven Transformers.

Neuromorphic vision is a bio-inspired technology that has triggered a paradigm shift in the computer vision community and is serving as a key enabler for a wide range of applications. This technology has offered significant advantages, including reduced power consumption, reduced processing needs, and communication speedups. However, neuromorphic cameras suffer from significant amounts of measurement noise. This noise deteriorates the performance of neuromorphic event-based perception and navigation algorithms. In this article, we propose a novel noise filtration algorithm to eliminate events that do not represent real log-intensity variations in the observed scene. We employ a graph neural network (GNN)-driven transformer algorithm, called GNN-Transformer, to classify every active event pixel in the raw stream into real log-intensity variation or noise. Within the GNN, a message-passing framework, referred to as EventConv, is carried out to reflect the spatiotemporal correlation among the events while preserving their asynchronous nature. We also introduce the known-object ground-truth labeling (KoGTL) approach for generating approximate ground-truth labels of event streams under various illumination conditions. KoGTL is used to generate labeled datasets, from experiments recorded in challenging lighting conditions, including moon light. These datasets are used to train and extensively test our proposed algorithm. When tested on unseen datasets, the proposed algorithm outperforms state-of-the-art methods by at least 8.8% in terms of filtration accuracy. Additional tests are also conducted on publicly available datasets (ETH Zürich Color-DAVIS346 datasets) to demonstrate the generalization capabilities of the proposed algorithm in the presence of illumination variations and different motion dynamics. Compared to state-of-the-art solutions, qualitative results verified the superior capability of the proposed algorithm to eliminate noise while preserving meaningful events in the scene.

Bacterial community shifts occur primarily through rhizosphere expansion in response to subsoil amendments.

To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled-environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense-clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep-banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant-mediated bacterial community response within the simulated dense-clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity.

Bacterial rarity in a subarctic stream network: Biodiversity patterns, assembly mechanisms and types of rarity.

Dendritic stream networks are an intriguing subject for exploring the spatial and temporal variability of the rare and common bacterial biosphere, yet very few such studies have been conducted. We sampled riverine bacterioplankton at 13 sites in a subarctic riverine network across 3 years, with five sampling times each year. Ordinations showed a consistent pattern of downstream shift for both rare and abundant subcommunities. We also detected a temporal signal, with seasonal community shifts reflecting changes in water temperature and groundwater contribution, and an inter-annual pattern where the year 2018 differed from other years. Phylogenetic turnover of the rare subcommunity indicated homogeneous selection, whereas the abundant subcommunity was mainly stochastically structured. Transiently rare taxa were the dominant type of rarity with the highest proportion at the headwater regions. The bacterioplankton community was characterized by a small group of core taxa that occurred at most sites with little temporal variation, a very large number of permanently or transiently rare taxa, and taxa shifting through time between the rare and abundant biosphere. While this basic structure could have been detected with less extensive temporal replication, a comprehensive understanding of the rare biosphere in riverine bacterioplankton can only be achieved via inter-annual, spatially replicated sampling that covers the whole stream network.

The Geologic History of Plants and Climate in India

India's diverse vegetation and landscapes provide an opportunity to understand the responses of vegetation to climate change. By examining pollen and fossil records along with carbon isotopes of organic matter and leaf wax, this review uncovers the rich vegetational history of India. Notably, during the late Miocene (8 to 6 Ma), the transition from C3 to C4 plants in lowland regions was a pivotal ecological shift, with fluctuations in their abundance during the late Quaternary (100 ka to the present). In India, the global phenomenon of C4 expansion was driven by the combined feedback of climate variations, changes in substrate conditions, and habitat disturbances. The Himalayan region has experienced profound transformations, including tree-line migrations, shifts in flowering and fruiting times, species loss, and shifts in plant communities due to changing monsoons and westerlies. Coastal areas, characterized by mangroves, have been dynamically influenced by changing sea extents driven by climate changes. In arid desert regions, the interplay between summer and westerlies rainfall has shaped vegetation composition. This review explores vegetation and climate history since 14 Ma and emphasizes the need for more isotope data from contemporary plants, precise sediment dating, and a better understanding of fire's role in shaping vegetation. ▪This review highlights diverse vegetation and landscapes of India as a valuable source for understanding the vegetation-climate link during the last 14 Myr.▪A significant ecological shift occurred during 8 to 6 Ma in India, marked by the transition from C3 to C4 plants in the lowland regions.▪The abundance of C3 and C4 plants varied in India during the late Quaternary (100 ka to present).▪This review emphasizes the importance of more isotope data, precise sediment dating, and a better understanding of fire's role in shaping vegetation.

Effects of different acidification-resisting strategies on anaerobic digestion of kitchen waste: Methanogenic properties and microbial community shift

Anaerobic digestion (AD) has been widely used as a promising technology for the treatment of kitchen waste (KW). The effects of several acidification-resisting methods were compared, which included the supplementation of trace elements (TEs) and zero-valent iron (ZVI) / powdered activated carbon (PAC), and the application of the sludge domesticated by acetic acid (HAc) and KW as inoculum. The results showed that the supplementation of TEs and ZVI/PAC at total solid (TS) content of 6% and optimal addition doses resulted in an increase in methane yield to 346 and 366 mL/g VS, respectively. In addition, the methane yields of 327 and 241 mL/g VS were obtained by applying the sludge domesticated with KW and HAc as inoculum, while the methane yield of the control was only 89.2 mL/g VS, representing a relative increase of 288%, 311%, 267%, and 170%. The acidification could be alleviated by applying these methods, and also the methanogenic profile was improved. Furthermore, microbial community analysis revealed that the enrichment of Methanosarcina, which enhanced the substrate utilization capacity and subsequently increased methane production, was achieved through the addition of TEs and ZVI/PAC, along with the application of sludge domesticated by KW.

Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints.

The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;43:1012-1029. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean.

The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.

Comparison of microbial communities and nitrite formation in two different beet sugar extraction systems

This study investigated nitrite formation in beet sugar factories, crucial due to tightening European Union directives for contaminants in feed material. Comparing two extraction systems (trough and tower), the trough system exhibited dynamic nitrite formation processes resulting in an average nitrite content of 14.35 mg/kg in raw juice. In the tower system, high nitrite levels and rapid degradation occurred in hot extraction areas, leading to an average nitrite content of 30.89 mg/kg in raw juice during sampling period. Microbial diversity analysis revealed a community shift, with Firmicutes dominating in hot extraction regions. Highly abundant amplicon sequence variants (ASVs) predominantly belonged to the genera Tuberibacillus and Geobacillus in both systems (Tuberibacillus: trough: 73%, tower: 67%; Geobacillus: trough: 41%, tower: 30%). Sequences related to bacteria relevant for nitrite metabolism varied between the two systems. Limosilactobacillus fermentum was more prevalent in the trough extraction system (6% relative abundance in raw juice), than in the tower system (0.5% relative abundance in raw juice). Similarly, Parageobacillus caldoxylolyticus was more abundant in tower extraction, especially in high-temperature zones like the countercurrent mixer (7% relative abundance). These findings provide insights into microbial processes, community structure, and potential strategies for early nitrite reduction in the extraction process.

Residual hydrocarbons in long-term contaminated soils: implications to risk-based management

Petroleum hydrocarbon (PHC) contamination is a widespread and severe environmental issue affecting many countries’ resource sectors. PHCs are mixtures of hydrocarbon compounds with varying molar masses that naturally attenuate at different rates. Lighter fractions attenuate first, followed by medium-molar-mass constituents, while larger molecules remain for longer periods. This results in significant regulatory challenges concerning residual hydrocarbons in long-term contaminated soils. This study examined the potential risks associated with residual PHC and its implications for risk-based management of heavily contaminated soils (23,000–26,000 mg PHC/kg). Ecotoxicological properties, such as seedling emergence and growth of two native plant species—small Flinders grass (Iseilema membranaceum) and ruby saltbush (Enchylaena tomentosa)—and earthworm survival tests in PHC-contaminated soils, were assessed. Additionally, the effects of aging on the attenuation of PHC in contaminated soils were evaluated. Toxicity responses of plant growth parameters were determined as no-observed-effect concentrations: 75%–100% for seedling emergence, < 25%–75% for plant shoot height, and 75%–100% for earthworm survival. After 42 weeks of aging, the total PHC levels in weathered soils decreased by 14% to 30% and by 67% in diesel-spiked soil due to natural attenuation. Dehydrogenase enzyme activity in soils increased during the initial aging period. Furthermore, a clear shift of bacterial communities was observed in the soils following aging, including enrichment of PHC-resistant and -utilizing bacteria—for example, Nocardia sp. This study underscores the potential of natural attenuation for eco-friendly and cost-effective soil management, underlining that its success depends on site-specific factors like water content and nutrient availability. Therefore, we recommend detailed soil assessments to evaluate these conditions prior to adopting a risk-based management approach.