Shifts In Bacterial Communities Research Articles

Generation of novel prebiotic oligosaccharide pools from fiber drives biological insight in bacterial glycan metabolism.

Prebiotic oligosaccharides are dietary supplements that modulate the intestinal gut microbiome by selectively nourishing subsets of the microbial community with a goal to enhance host health. To date, the diversity of polysaccharide compositions in the fiber consumed by humans is not well represented by the limited scope of oligosaccharide compositions present in current commercial prebiotics. Recently, our UC Davis group developed a novel method to generate oligosaccharides from any polysaccharide fiber, termed Fenton's Initiation Toward Defined Oligosaccharide Groups (FITDOG). Using this method, sugar beet pulp (SBP) was transformed into sugar beet oligosaccharides (SBOs) composed of arabinose- and galactose-containing oligosaccharides. Fecal fermentations of SBO and SBP produced similar shifts in donor-specific bacterial communities and acid metabolite profiles with a general enrichment of Bacteroides and Bifidobacterium. However, in vitro tests revealed more Bifidobacterium strains could consume SBO than sugar beet arabinan, and specific strains showed differential consumption of arabinofuranooligosaccharides or galactooligosaccharide (GOS) portions of the SBO pool. Genomic and glycomic comparisons suggest that previously characterized, arabinan-specific, extracellular arabinofuranosidases from Bifidobacterium are not necessary to metabolize the arabino-oligosaccharides within SBO. Synbiotic application of SBO with an SBO-consuming strain Bifidobacterium longum subsp. longum SC596 in serial fecal enrichments resulted in enhanced persistence among 9 of 10 donor feces. This work demonstrates a novel workflow whereby FITDOG creates novel oligosaccharide pools that can provide insight into how compositional differences in fiber drive differential gut fermentation behaviors as well as their downstream health impacts. Moreover, these oligosaccharides may be useful in new prebiotic and synbiotic applications.IMPORTANCEPrebiotics seek to selectively alter the host microbiome composition or function, resulting in a concurrent health benefit to the host. However, commercial prebiotics represent a small fraction of the diversity of food polysaccharide compositions. In this work a novel method, Fenton's Initiation Toward Defined Oligosaccharide Groups (FITDOG) was used to generate an oligosaccharide pool from sugar beet pulp (SBP). Sugar beet oligosaccharides (SBOs) resulted in similar changes to SBP in fecal enrichments; however, SBO could be consumed by more beneficial bifidobacterial strains than the cognate polysaccharide. These results demonstrate how the details of glycan structure have a profound influence on how gut bacteria metabolize food carbohydrates. The implications of this work are relevant to understanding how different dietary sources influence the human microbiome and extend to developing novel oligosaccharide pools for prebiotic applications.

Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession

Abstract Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the temporal variation in the soil- versus root-associated microbiome over plant species turnover during secondary succession has rarely been quantified. Using the chronosequence restored from fenced grassland and abandoned farmlands on the Loess Plateau of China, we characterized the dynamics of the soil- and root-associated microbiome of host plant with different dominance statuses during secondary succession from 0 to 40 years. Our results revealed that the root microhabitat, the host plant and their interactions were the main contributors to the bacterial community shift (R2 = 15.5%, 8.1% and 22.3%, respectively), and plant interspecies replacement had a greater effect on the shift in the root-associated microbial community than intraspecies replacement did during succession. The root-associated bacterial community of pioneer plants was particularly responsive to succession, especially the endosphere community. Endosphere microbial diversity was positively correlated with host plant coverage change, and the diversity and abundance of taxon recruitment into the endosphere of pioneer plants from the surrounding environment decreased as succession progressed. The community assembly processes also indicated that the endosphere microbiota are strongly selected in younger host plants, whereas stochastic processes dominate in aged host plants. Our study provides evidence of the unique response of the root-associated microbiome to the replacement of plant species during secondary succession, and the function of endosphere microbes should be considered when studying plant–microbe feedback.

Responses of Soil Microbial Communities to Abandoned Paddy Fields With Different Fertilization Histories

ABSTRACTThe abandonment of cultivated fields notably affects soil characteristics. However, its impact on soil microbial community composition, particularly under different fertilization regimes, remains poorly understood. Therefore, we evaluated the effects of abandoned paddy fields with different fertilization histories (no fertilization, NK, NP, and NPK) on the abundance, composition, and their predicted function of soil bacteria and fungi. Our findings revealed that the abandonment led to a considerable decrease in soil bacterial and fungal biomass. Fertilization history and abandonment each significantly affected on the bacterial community, resulting in increased relative proportions of Acidobacteria and decreased relative proportions of Proteobacteria in the NP and NPK treatments compared to those in the CK and NK treatments. The fungal community only exhibited a notable response to abandonment, with variations in the relative abundance of Ascomycota, Mucoromycota, and Basidiomycota. Canonical correspondence analysis revealed the significant association between soil bacterial community and pH, total phosphorus, and available phosphorus, whereas the pH and NO3−–N were key drivers of fungal community variations in abandoned soils. Network analysis indicated that abandonment enhanced the complexity but decreased the stability of the bacterial community, while fungi exhibited the opposite trend. Our findings highlight that changes in bacterial functions caused by residual nutrients, particularly high residual phosphorus, may accelerate soil organic C decomposition. Overall, this study provides a novel insight into the shifts in soil bacterial and fungal communities and their ecological functions after the abandonment of cultivated fields.

Comparative soil bacterial metabarcoding after aboveground vs. subsurface decomposition of Mus musculus

Outdoor microcosms, metabarcoding with next-generation sequencing of the 16S rRNA bacterial gene, total body score (TBS) and physicochemical analyses were used to monitor Mus musculus decomposition aboveground (A) and in the subsurface (S), and compared to soil-only controls (C). As determined by MaAsLin2 analysis, significant shifts in bacterial communities at 30 cm depths within the A, S and C treatments distinguished control from experimental soils, and between aboveground and subsurface deposition, demonstrating the potential for gravesoil discrimination during the first 90 days. For example, Dokdonella (p = 0.0002), Edaphobaculum (p = 0.0004) and Lacibacter (p = 0.0034) recorded significant shifts relative to sampling time. Furthermore, Massilia (p = 0.0005), Mycobacterium (p = 0.0006) and Sandaracinus (p = 0.0007) increased in abundance for the aboveground mice treatments. This was confirmed with ANOSIM where p = 0.0082 showed statistically significant difference between the aboveground and subsurface deposition. TBS and physicochemical analyses suggested that nutrient release into the soils occurred during active decay and skin rapture on days 7–13 in the subsurface and days 13–20 aboveground, with a particular increase in soil potassium concentration on day 15. Significant differences in soil temperatures resulted between A and S vs. C microcosms, aligning with atmospheric temperature changes. In summary, complementary application of metabarcoding, total body score, exogenous and physicochemical methods for postmortem interval estimation and clandestine grave location highlighted the feasibility of using temperature records downloaded from meteorological stations and portable X-ray fluorescence as indicators for various phases of decomposition.

Unfolding the Roles of Particulate- and Mineral-Associated Organic Carbon in Soil Microbial Communities

Forest succession is a rapid approach that can be used to increase soil carbon (C) stocks. It is crucial to understand how forest succession influences microbial community assembly and soil carbon fractions to improve carbon sequestration strategies. This present work analyzed microbial communities in forest succession, and the effects of particulate-associated organic C (POC) and mineral-associated organic C (MAOC) on microbial community structure and assembly in forest succession in Changbai Mountains, China. Compared to cropland, primary forest increased MAOC by 35% and POC by 43%, suggesting the importance of POC for microbial assembly processes, offering insights into forest restoration practices to enhance soil carbon sequestration. As succession proceeds, weak environmental selection facilitated the reduced deterministic processes, whereas local ecological and dispersal drift were elevated. Such shifts in fungal and bacterial communities could be mostly triggered by soil pH. Considering that POC was important, shifts in assembly processes can be determined by resource availability rather than succession sequences. Such findings conform to the neutral hypothesis, suggesting that POC exerts a negligible effect on analyzing microbial community assembly in forest succession. Overall, this present work sheds more light on the important effects of POC and MAOC on modeling different microbial communities and community assembly in forest succession.

Different Nutritional Regimes in a Tomato Soilless System Affect the Bacterial Communities with Consequences on the Crop Quality

This study investigates the impact of different nutritional regimes on the bacterial communities within the root-growing substrate of a soilless tomato production system and the effects on crop quality. The experiment was conducted with two tomato varieties, Conchita and Sweetelle, under three nutritional treatments: standard, nutrient solution with 20% increased salts and nitrogen and supplementation with the biostimulant Bio-algeen S-90. Bacterial communities in the root substrate were influenced by both the tomato variety and the nutritional regime. Sweetelle exhibited more pronounced shifts in bacterial communities compared to Conchita. An overall increase in bacterial populations with time was observed (+0.38 Log). Specifically, the 20% enhanced nutrient solution had varying effects on bacterial counts in the two tomato varieties, while the biostimulant promoted an increase in ammonia-oxidizing bacteria (+0.4 Log). Microbial community analysis highlighted the distinct impact of each nutritional regime on nitrogen-cycling bacteria, which correlated with differences in quality parameters such as the L-ascorbic acid and lycopene contents. In the first case, a decrease (25–30%) was observed, while the lycopene content decreased after harvest (−51% in Conchita variety) but was more stable in the postharvest phase (66–70% lycopene retained, only 44% in the control). This study highlights how increased sources of nutrients and the differential responses of microbial communities to nutritional regimes do not necessarily increase the crop quality and that tailored approaches are required for different tomato varieties.

Synergizing carbon sequestration mechanisms during the remediation of Cr(VI) by nano zero-valent iron loaded biochar (nZVI-BC)

Applying nano zero-valent iron loaded biochar (nZVI-BC) to remediate soil heavy metal pollution has been frequently tested in current studies. However, little knowledge has been disclosed regarding the effect of nZVI-BC on soil organic carbon (SOC) mineralization/sequestration. In this study, the dual effect of nZVI-BC addition on Cr(VI) removal and SOC mineralization/sequestration and the underlying mechanisms were explored, based on a 90 days laboratory soil incubation. The results confirmed that nZVI-BC significantly improved the Cr(VI) removal rate while markedly reducing the cumulative CO2 emissions. Following the 90 days incubation, nZVI-BC addition notably increased the contents of Fe-oxides, Fe-bound organic carbon (Fe-OC), and SOC. Pearson correlation and PLS-SEM analyses indicated that the enhanced Fe-OC content, resulting from increased Fe-oxides, was a critical abiotic mechanism for improved SOC preservation. Additionally, the observed decrease in enzymatic activity and the shift in bacterial community from unstable carbon-dominant taxa (e.g., Proteobacteria and Actinobacteria) to stable carbon-dominant taxa (e.g., Firmicutes) in the nZVI-BC treatments suggested that SOC bio-mineralization was also inhibited. Overall, this study demonstrates that nZVI-BC not only aids in heavy metal remediation but also promotes long-term SOC preservation.

Microbiota responses to mutations affecting NO homeostasis in Arabidopsis thaliana.

Interactions between plants and microorganisms are pivotal for plant growth and productivity. Several plant molecular mechanisms that shape these microbial communities have been identified. However, the importance of nitric oxide (NO) produced by plants for the associated microbiota remains elusive. Using Arabidopsis thaliana isogenic mutants overproducing NO (nox1, NO overexpression) or down-producing NO (i.e. nia1nia2 impaired in the expression of both nitrate reductases NR1/NIA1 and NR2/NIA2; the 35s::GSNOR1 line overexpressing nitrosoglutathione reductase (GSNOR) and 35s::AHB1 line overexpressing haemoglobin 1 (AHB1)), we investigated how altered NO homeostasis affects microbial communities in the rhizosphere and in the roots, soil microbial activity and soil metabolites. We show that the rhizosphere microbiome was affected by the mutant genotypes, with the nox1 and nia1nia2 mutants causing opposite shifts in bacterial and fungal communities compared with the wild-type (WT) Col-0 in the rhizosphere and roots, respectively. These mutants also exhibited distinctive soil metabolite profiles than those from the other genotypes while soil microbial activity did not differ between the mutants and the WT Col-0. Our findings support our hypothesis that changes in NO production by plants can influence the plant microbiome composition with differential effects between fungal and bacterial communities.

Does Antibiotic Use Contribute to Biofilm Resistance in Sink Drains? A Case Study from Four German Hospital Wards.

Backgound. As biofilms are known to harbour (multi-)resistant species, their presence in health settings must be considered critical. Although there is evidence that bacteria spread from drains to the outside, there is still a lack of research data focusing on drain biofilms from hospitals. Methods. We sampled biofilms from various wards of Helios Hospital Krefeld (Germany), where comprehensive antibiotic consumption data were available. Biofilms were analysed by cell counting, isolation of relevant bacterial groups and genetic and phenotypical resistance parameters. Data were correlated with the prescribed antibiotics of the respective ward. Furthermore, an ex situ biofilm model was employed to investigate the influence of sub-inhibitory antibiotics on the bacterial community and the prevalence of class 1 integrons. Results. Our results show that every ward harboured medically relevant bacterial species. While no significant differences were found in cell counts, the median prevalence of the resistance marker gene intI1 correlated with the amount of prescribed antibiotics. In contrast, phenotypical resistances showed no similar tendency. In addition, melting curve analysis data and changes in intI1 prevalence show that the composition of the bacterial community shifted depending on the biofilm and antibiotic. Conclusions. To the best of our knowledge, our study is the first considering possible correlations between the consumption data of hospital wards and resistances in drain biofilms the way we did. Based on our results, we conclude that sub-inhibitory concentrations of antibiotics have no general effect on biofilms in terms of bacterial community shift and occurrence of antibiotic-resistant species. Amongst other things, the effect depends on the initial composition of the bacterial community, the antibiotic used and the intrinsic bacterial resistance, e.g., prevalence of class 1 integrons.

Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics

Climate change has significantly affected the subalpine ecosystems, leading to mass die-offs of the Korean fir tree, a key climate-sensitive species in these environments. Proactive analysis of the phenotypic responses of these trees to climate change or the establishment of preemptive strategies for trees to adapt to these environmental changes remains a challenge. The current study aimed to investigate the impact of climate change on the health of Korean fir (Abies koreana) in the subalpine ecosystem of Jirisan Mountain, South Korea. We integrated soil physicochemical analyses, microbial community dynamics, neutral community model, and network analyses to examine the relationships between tree health and microbial communities. Our findings revealed significant changes in soil chemical properties, including pH and nutrient concentrations, across the various health statuses of trees. Microbial community analysis demonstrated shifts in bacterial and fungal communities corresponding to the health continuum of the trees, with decreased diversity and altered composition in the declining trees. A remarkable increase in modularity of the microbial network and a clear transition from stochastic to deterministic microbial community assembly processes were observed as the trees progressed from a healthy to a dead stage. Two bacterial genera, Bradyrhizobium and Burkholderia, along with an unclassified fungal group from Basidiomycota, were identified as key microbial indicators of good tree health. This study highlighted the importance of microbial communities as bioindicators for assessing the health of subalpine ecosystem and its resilience to climate change, offering valuable insights into the conservation and management strategies for subalpine ecosystems.

Choice of activated sludge microorganisms under phosphate deficiency: Competition for inorganic phosphate or change to organophosphorus metabolism

Phosphorus (P) plays a crucial role in the microbial processes of wastewater treatment. However, the current understanding of P metabolic pathways in wastewater is incomplete, and the mechanisms of microbial P metabolism under P deficient conditions remain unclear. This study explores the succession patterns of activated sludge bacterial communities and their potential P utilization strategies under P-deficient conditions. The results indicate that changes in phosphorus concentration and composition drive microbial community succession. Under P deficiency, microorganisms initially focus on inorganic phosphorus (IP) metabolism, prioritizing competition for IP. Subsequently, the bacterial community shifts to predominantly utilizing organic phosphorus (OP), with over 94% of genomes carrying OP metabolism genes. The OP in the system primarily consists of phosphonates and phosphoester. Consequently, distinct bacterial responses to phosphoester and phosphonates were observed, with the bacterial community transitioning from low modular to highly modular communities with differentiated niches. Phosphoester and phosphonate metabolism emerged as the two main OP metabolic pathways within the community. By reconstructing the P metabolic pathways of dominant genera, including Pannonibacter (Proteobacteria) and f_Saprospiraceae (Bacteroidota), metabolic models of phosphonate and phosphoester were developed in a wastewater treatment system for the first time. This study provides new insights into biological P metabolism in wastewater treatment, expanding our understanding of P metabolic pathways in wastewater.

Host genotype and infection status interact to shape microbiomes in Daphnia magna.

Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

Grazing disturbance reduces biocrust-related cyanobacteria and N-fixer abundance but increases bacterial diversity: Implications for biocrust restoration in degraded drylands

Overgrazing is a major driver of dryland degradation, however, so far, there is limited understanding on how this process affects biocrust-related microbial community, and especially how the key groups respond to grazing disturbance. In this study, quantitative polymerase chain reaction (qPCR) and high throughout sequencing technologies were used to investigate the bacterial community abundance and diversity in the Horqin Sandland (China) experiencing different livestock grazing disturbances, in order to examine whether a shift in bacterial community (in particular the key biocrust components, cyanobacteria) was involved, and how this was related to biocrust development and altered soil carbon and nitrogen level. Our results revealed that a clear heterogeneous soil bacterial community was associated with grazing disturbance, which inhibited biocrust development. The decreased photosynthetic cyanobacterial abundance (81.81 % in relative abundance and 98.83 % in absolute abundance) and nitrogen-fixing genes (87.72 %), associated with the lower total carbon and nitrogen content (P<0.05), illustrated a low soil carbon and nitrogen-fixing capability and nutrient level in the grazing-disturbed soils. In particular, a switch of nitrogen-fixing dominance from cyanobacteria to proteobacteria was induced by the grazing disturbance. Compared to the grazing-disturbed soils, higher dominant cyanobacterial operational taxonomic units (OTUs) (especially the species of Nostoc and Scytonema) and lower bacterial diversity (e.g., Shannon, Ace, and Chao index) were observed in the undisturbed biocrust soils, highlighting that the dominants rather than diversity played more important roles in biocrust development. Collectively, our results demonstrate that cyanobacteria are very sensitive (even more than others, e.g., proteobacteria and actinobacteria) to grazing disturbance, therefore, we propose that cyanobacterial inoculation is likely an effective approach to supplement soil cyanobacterial abundance, which is expected to induce biocrust development and increase carbon and nitrogen level in the disturbed drylands.

Aerobic granular sludge enhances start-up and granulation in single-stage partial nitritation anammox granular sludge systems: Performance, mechanism, and shifts in bacterial communities

The rapid start-up and granulation of a single-stage partial nitritation anammox granular sludge (PN/AnGS) system under limited seed sludge conditions is crucial for its practical application. This study proposed an aerobic granular sludge (AGS) − based strategy, enhanced the enrichment of anammox bacteria (AnAOB), and shortened the start-up time of PN/AnGS system by 20.5%. In addition, the inoculation of AGS can ensure the stable operation of the system during the selective sludge discharge to washout the flocs. Microbial community structure, particle size distribution, morphology results showed that niche shift was the key to promote the enrichment of AnAOB, and AGS played a decisive role in the particle characteristics of PN/AnGS. Since AGS can be directly obtained from full-scale AGS wastewater treatment plants, integrating PN/AnGS with AGS processes can transition wastewater treatment from a “linear economy” to a “circular economy”, enhancing nitrogen removal efficiency and delivering significant economic and environmental benefits.

Degradation of oxytetracycline in soil by a Pseudomonas strain

Oxytetracycline (OTC) is used extensively in animal husbandry and enters the soil in different forms, causing severe environmental pollution. Previous studies have shown that the genus Pseudomonas can potentially degrade antibiotics in the soil environment. Environmental conditions, such as the initial concentration of antibiotics, incubation temperature and others, have significant impacts on the activity of antibiotic-degrading bacteria. However, few reports have clarified the environmental impacts on the effectiveness of Pseudomonas spp. In the present study, we investigated the effects of different initial concentrations of OTC and incubation temperatures, as well as soil sterilization, on OTC degradation by Pseudomonas <pg=>strain T4. We also focused on the microbial degradation pathways of OTC, and variations in both antibiotic resistance genes (ARGs) and microbial communities with T4 functioning under optimal conditions. The results showed that the most effective degradation occurred under an initial OTC concentration of 2.5 mg kg-1 at 30°C in unsterilized soil spiked with T4. These conditions yielded an OTC degradation rate of 69.53% within 63 days. The putative degradation pathways of OTC in the presence of T4 included dehydration, demethylation, deamination, hydroxylation, oxidation and ring opening. Bacteroidetes, Proteobacteria and Acidobacteria played key roles in the biodegradation of OTC with T4 in the soil. The results also showed that tet(G) was the most frequently detected among the 13 common tetracycline ARGs that were investigated. The bacterial community shift observed in this study may provide new insights into the microbial degradation of OTC in soil.

Shift of bacterial and fungal communities upon soil amelioration is driven by carbon degradability of organic amendments

The structural response of bacterial and fungal soil communities to four carbon-rich organic amendments of increasing recalcitrance was investigated. Wheat straw, green compost, a mixed product based on biogas residues, and a fermented biochar were applied to a sandy agricultural soil of low organic carbon content. After laboratory incubation for 6 months, the community structure was investigated via DNA sequencing. All amendments caused changes in the communities of bacteria and fungi, but to different extents, with the communities exposed to more recalcitrant amendments showing the least variation compared to the non-amended soil. Changes in species composition as well as their relative abundances were observed. While the straw had a pronounced effect on bacteria (e.g., the highest number of indicator species), effects of the composted, fermented, or pyrolyzed materials were minor. Hierarchical clustering showed that the fungal communities were more different from each other than the bacterial ones with the straw-soil being most different and the biochar-soil least different from the non-amended soil. While the abundant fungal species in biochar-soil and non-amended soil were very alike, especially rare fungal species shifted upon addition of biochar. An indicator species analysis identified specific taxonomic groups which were triggered by the different organic materials. We conclude that bacterial and fungal communities strongly change upon input of degradable carbon (straw), while fungi in particular respond to the application of processed organic materials. With this study, we report the consequences of applying organic materials for the microbial community in one soil. We provide these data for meta-analyses that are required to unravel all relevant interactions across different soils, organic materials, and time. This will allow to better understand and predict the effects of organic soil amelioration measures on soil microorganisms.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

Moisture-mineral interactions drive bacterial and organic matter turnover in glacier-sourced riparian sediments undergoing pedogenesis

Glacial recession is occurring at unprecedented rates resulting in increased sediment accumulations in some riverine ecosystems providing new mineral surfaces for soil formation. Soils and sediments have an enormous potential to retain carbon (C), predominantly due to sorption to mineral surfaces. However, C persistence may be sensitive to climate-change induced temperature and moisture variations. We coupled ultrahigh resolution organic matter composition classification with bacterial characterization and respiration measurements to test the combined pedogenic effects of temperature (4 vs 20 °C) and moisture (50 vs 100% water-filled pore space) on C turnover in sediments maintained under different mineralogical conditions (illite-amended vs non-amended). Here we show that the inhibition of CO2 emissions from the combined effect of increased moisture content and illite was reflected in the turnover of key molecular signatures, such as the nominal oxidation state of C, often irrespective of temperature. However, shifts in bacterial communities from a coupled moisture-mineral interaction, were temperature-dependent. Our results highlight the importance of moisture in driving mineral-organic interactions and suggest that C in clay-rich, water-saturated sediments is both thermodynamically unfavorable and mineral-protected from microbial consumption.

The microbiome of continuous wheat rotations: minor shifts in bacterial and archaeal communities but a source for functionally active plant-beneficial bacteria

Continuous wheat cropping often leads to yield decline, with suspected causes including increased pathogen susceptibility, decreased root growth, or low nutrient use efficiency, though the exact causes remain unknown. Here, we investigated soil and root-associated bacterial and archaeal communities in wheat under rotation versus continuous cultivation, monitored fungal pathogen presence, and used beneficial bacteria to mitigate Gaeumannomyces tritici (Ggt) symptoms in greenhouse experiments. Sampling was conducted at two field sites with different soil textures over two years and at two plant developmental stages, capturing site-specific and seasonal fluctuations. By cultivation, 767 bacterial isolates were screened for plant-beneficial traits. Amplicon sequencing revealed minor effects on community structure due to wheat rotational position but pronounced effects related to site, year, and microhabitat. Rhizoplane isolates with plant-beneficial traits were mainly Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Stenotrophomonas, and Variovorax. Continuous wheat rotations showed the highest proportion of bacteria with fungal antagonistic potential, indicating plant roots’ recruitment of beneficial bacteria. Introducing Ggt in the greenhouse experiment altered the bacterial and archaeal community, confirming field study results and demonstrating that applying beneficial bacteria early in the season at the seedling stage can control Ggt and improve plant growth. This study highlights the dynamic nature of wheat's below-ground bacterial and archaeal community, influenced by soil type, season, and microhabitat, with wheat rotation playing a minor role. In addition, it confirms the potential of selected Bacillus and Pseudomonas isolates, whether used individually or in consortia, for microbe-assisted mitigation of yield decline in intensive wheat production.

Effects of fructan and gluten on gut microbiota in individuals with self-reported non-celiac gluten/wheat sensitivity—a randomised controlled crossover trial

BackgroundIndividuals with non-celiac gluten/wheat sensitivity (NCGWS) experience improvement in gastrointestinal symptoms following a gluten-free diet. Although previous results have indicated that fructo-oligosaccharides (FOS), a type of short-chain fructans, were more likely to induce symptoms than gluten in self-reported NCGWS patients, the underlying mechanisms are unresolved.MethodsOur main objective was therefore to investigate whether FOS-fructans and gluten affect the composition and diversity of the faecal microbiota (16S rRNA gene sequencing), faecal metabolites of microbial fermentation (short-chain fatty acids [SCFA]; gas chromatography with flame ionization detector), and a faecal biomarker of gut inflammation (neutrophil gelatinase-associated lipocalin, also known as lipocalin 2, NGAL/LCN2; ELISA). In the randomised double-blind placebo-controlled crossover study, 59 participants with self-reported NCGWS underwent three different 7-day diet challenges with gluten (5.7 g/day), FOS-fructans (2.1 g/day), and placebo separately (three periods, six challenge sequences).ResultsThe relative abundances of certain bacterial taxa were affected differently by the diet challenges. After the FOS-fructan challenge, Fusicatenibacter increased, while Eubacterium (E.) coprostanoligenes group, Anaerotruncus, and unknown Ruminococcaceae genera decreased. The gluten challenge was primarily characterized by increased abundance of Eubacterium xylanophilum group. However, no differences were found for bacterial diversity (α-diversity), overall bacterial community structure (β-diversity), faecal metabolites (SCFA), or NGAL/LCN2. Furthermore, gastrointestinal symptoms in response to FOS-fructans were generally not linked to substantial shifts in the gut bacterial community. However, the reduction in E. coprostanoligenes group following the FOS-fructan challenge was associated with increased gastrointestinal pain. Finally, correlation analysis revealed that changes in gastrointestinal symptoms following the FOS-fructan and gluten challenges were linked to varying bacterial abundances at baseline.ConclusionsIn conclusion, while FOS-fructans induced more gastrointestinal symptoms than gluten in the NCGWS patients, we did not find that substantial shifts in the composition nor function of the faecal microbiota could explain these differences in the current study. However, our results indicate that individual variations in baseline bacterial composition/function may influence the gastrointestinal symptom response to both FOS-fructans and gluten. Additionally, the change in E. coprostanoligenes group, which was associated with increased symptoms, implies that attention should be given to these bacteria in future trials investigating the impact of dietary treatments on gastrointestinal symptoms.Trial registrationClinicaltrials.gov as NCT02464150.