Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes

Seasonal effects of long-term warming on ecosystem function and bacterial diversity

Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

Bacteria face trade-offs in the decomposition of complex biopolymers

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.

A Marine Group A isolate relies on other growing bacteria for cell wall formation

Most of Earth's prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or 'Candidatus Marinimicrobia') that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria. Reliance on exogenous muropeptides is traceable to the phylum's ancestor, with evidence of vertical inheritance across several classes. This dependency may be widespread across bacteria (16 phyla) based on the absence of key peptidoglycan synthesis genes. These results suggest that uptake of exogenous cell wall components could be a relevant and potentially common survival strategy in energy-limited habitats like the deep biosphere.

Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea

The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.

Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders

Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity.

IMPORTANCE

New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

Gastrointestinal response to the early administration of antimicrobial agents in growing turkeys infected with Escherichia coli

This study investigated the effects of the early administration of enrofloxacin (E) or doxycycline (D) for the first 5 consecutive days of life, or the continuous administration of the coccidiostat monensin (M) throughout the rearing period on gastrointestinal function in turkeys infected with avian pathogenic Escherichia coli (APEC) in an early or later stage of rearing. Experiment 1 lasted 21 d, and turkeys in groups E, D, and M were infected with APEC on d 15. Experiment 2 lasted 56 d, and it had a factorial arrangement of treatments where birds in groups E, D, and M were infected with APEC on d 15 or d 50. In both experiments, control groups (C) consisted of infected and uninfected birds without antibiotic or coccidiostat administration. On d 21 (Experiment 1) and d 56 (Experiment 2), 8 birds from each subgroup were killed, and the ileal and cecal digesta were sampled to analyze the activity of bacterial enzymes and the concentrations of short-chain fatty acids (SCFA). The experimental treatments did not affect the final body weight or body weight gain of birds. Both experiments demonstrated that APEC contributed to an increase in ammonia levels of the cecal digesta (means from 2 experiments: 0.311 vs. 0.225 mg/g in uninfected birds) and ileal pH (6.79 vs. 6.00) and viscosity (2.43 vs. 1.83 mPa⋅s). Moreover, the E. coli challenge enhanced the extracellular activity of several cecal bacterial enzymes, especially in older turkeys infected with APEC in a later stage of life. The continuous administration of monensin throughout the rearing period resulted in a weaker gastrointestinal response in older birds, compared with the other 2 antibiotics administered for the first 5 d of life. The results of the study are inconclusive as both desirable and undesirable effects of preventive early short-term antibiotic therapy were observed in turkeys, including normalization of ileal viscosity and cecal ammonia concentration (positive effect), and disruption in cecal SCFA production (negative effect).

Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future

Cancer, ranked as the second leading cause of mortality worldwide, leads to the death of approximately seven million people annually, establishing itself as one of the most significant health challenges globally. The discovery and identification of new anti-cancer drugs that kill or inactivate cancer cells without harming normal and healthy cells and reduce adverse effects on the immune system is a potential challenge in medicine and a fundamental goal in Many studies. Therapeutic bacteria and viruses have become a dual-faceted instrument in cancer therapy. They provide a promising avenue for cancer treatment, but at the same time, they also create significant obstacles and complications that contribute to cancer growth and development. This review article explores the role of bacteria and viruses in cancer treatment, examining their potential benefits and drawbacks. By amalgamating established knowledge and perspectives, this review offers an in-depth examination of the present research landscape within this domain and identifies avenues for future investigation.

Mechanisms of microbial-driven changes in soil ecological stoichiometry around gold mines

In this study, we used soils with different pollution and nutrient levels (non-polluted S1, highly polluted low-nutrient S2, and highly polluted high nutrient S3) around the gold mine tailing ponds, and combined with metabolic limitation modeling and macro-genomics approaches, aiming to investigate the relationship between soil microbial composition and soil eco-chemometrics characteristics under heavy metal stress. The results showed that heavy pollution resulted in reduced SOC, TN, microbial biomass, and with C- and P- acquisition (BG, CBH, ALP) as well as nitrogen limitation of soil microbial metabolism in soils (S2, S3). Further analysis by macrogenomics showed that heavy metal contamination led to an increase in α-microbial diversity and altered the composition of microbial communities in the soil. The cycling of C, N, and P nutrients was altered by affecting the relative abundance of Anaeromyxobacter, Steroidobacter, Bradyrhizobium, Acidobacterium, Limnochorda (predominantly in the Ascomycetes and Acidobacteria phyla), with the most pronounced effect on the composition of microorganisms synthesizing C-acquiring enzymes, and heavy metals and pH were the main influences on ecological stoichiometry. The results of this study are useful for understanding the sustainability of ecological remediation in heavy metal contaminated areas and for developing ecological restoration strategies.

Two-way NxP fertilisation experiment on barley (Hordeum vulgare) reveals shift from additive to synergistic N-P interactions at critical phosphorus fertilisation level

In a pot experiment, we investigated synergistic interaction of N and P fertilisation on barley biomass (Hordeum vulgare) on both shoot and root level with the aim to determine whether N-P interaction would be the same for all levels of N and P fertilisation. We further aimed to determine whether there was a critical level of N and/or P fertilisation rate, above which, a decrease in resource allocation to roots (as nutrient availability increased) could be demonstrated. Barley plants were grown from seed on a nutrient poor substrate and subjected to a two-way NxP fertilisation gradient using a modified Hoagland fertilisation solution. We observed N-P interactions in shoot and root biomass, and N and P use-efficiencies. A synergistic response in biomass was observed only above a critical level of P fertilisation when P was not limiting growth. Furthermore, we found that the same incremental increase in N:P ratio of applied fertiliser elicited different responses in shoot and root biomass depending on P treatment and concluded that barley plants were less able to cope with increasing stoichiometric imbalance when P was deficient. We provide, for the first time, stoichiometric evidence that critical levels for synergistic interactions between N-P may exist in crop plants.

Designing phage cocktails to combat the emergence of bacteriophage-resistant mutants in multidrug-resistant Klebsiella pneumoniae

IMPORTANCE

In this study, we aimed to design a novel and effective bacteriophage cocktail that can target both wild-type bacteria and phage-resistant mutants. To achieve this goal, we isolated four phages (U2874, phi_KPN_H2, phi_KPN_S3, and phi_KPN_HS3) that recognized different bacterial surface molecules using phage-resistant bacteria. We constructed three phage cocktails and tested their phage resistance-suppressing ability against multidrug-resistant Klebsiella pneumoniae. We argue that the phage cocktail that induces resensitization of phage susceptibility exhibited superior phage resistance-suppressing ability. Moreover, we observed trade-off effects that manifested progressively in phage-resistant bacteria. We hypothesize that such trade-off effects can augment therapeutic efficacy. We also recommend collating phage host range data against phage-resistant mutants in addition to wild-type bacteria when establishing phage banks to improve the efficiency of phage therapy. Our study underscores the importance of phage host range data in constructing effective phage cocktails for clinical use.

Performance and robustness analysis reveals phenotypic trade-offs in yeast

To design strains that can function efficiently in complex industrial settings, it is crucial to consider their robustness, that is, the stability of their performance when faced with perturbations. In the present study, we cultivated 24 Saccharomyces cerevisiae strains under conditions that simulated perturbations encountered during lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The observed negative correlations confirmed a trade-off between performance and robustness of ethanol yield, biomass yield, and cell dry weight. Conversely, the specific growth rate performance positively correlated with the robustness, presumably because of evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in the tested perturbation space. Our results experimentally map the robustness-performance trade-offs, previously demonstrated mainly by single-phenotype and computational studies.

r/K selection of GC content in prokaryotes

The guanine/cytosine (GC) content of prokaryotic genomes is species-specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC-content prokaryotes are r-strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K-strategists specialized for stable environments that maintain homeostasis via a high-cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient-to-biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC-rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.

Phylogenetically related soil actinomycetes distinguish isolation sites by their metabolic activities

Soil environments are inhabited by microorganisms adapted to its diversified microhabitats. The metabolic activity of individual strains/populations reflects resources available at a particular spot, quality of which may not comply with broad soil characteristics. To explore the potential of individual strains to adapt to particular micro-niches of carbon sources, a set of 331 Actinomycetia strains were collected at ten sites differing in vegetation, soil pH, organic matter content and quality. The strains were isolated on the same complex medium with neutral pH and their metabolites analyzed by UHPLC and LC-MS/MS in spent cultivation medium (metabolic profiles). For all strains, their metabolic profiles correlated with soil pH and organic matter content of the original sites. In comparison, strains phylogeny based on either 16S rRNA or the beta-subunit of DNA-dependent RNA polymerase (rpoB) genes was partially correlated with soil organic matter content but not soil pH at the sites. Antimicrobial activities of strains against Kocuria rhizophila, Escherichia coli, and Saccharomyces cerevisiae were both site- and phylogeny-dependent. The precise adaptation of metabolic profiles to overall sites characteristics was further supported by the production of locally specific bioactive metabolites and suggested that carbon resources represent a significant selection pressure connected to specific antibiotic activities.

Drivers of microbially and plant-derived carbon in topsoil and subsoil

Plant- and microbially derived carbon (C) are the two major sources of soil organic matter (SOM), and their ratio impacts SOM composition, accumulation, stability, and turnover. The contributions of and the key factors defining the plant and microbial C in SOM along the soil profile are not well known. By leveraging nuclear magnetic resonance spectroscopy and biomarker analysis, we analyzed the plant and microbial C in three soil types using regional-scale sampling and combined these results with a meta-analysis. Topsoil (0-40 cm) was rich in carbohydrates and lignin (38%-50%), whereas subsoil (40-100 cm) contained more proteins and lipids (26%-60%). The proportion of plant C increases, while microbial C decreases with SOM content. The decrease rate of the ratio of the microbially derived C to plant-derived C (CM:P ) with SOM content was 23%-30% faster in the topsoil than in the subsoil in the regional study and meta-analysis. The topsoil had high potential to stabilize plant-derived C through intensive microbial transformations and microbial necromass formation. Plant C input and mean annual soil temperature were the main factors defining CM:P in topsoil, whereas the fungi-to-bacteria ratio and clay content were the main factors influencing subsoil CM:P . Combining a regional study and meta-analysis, we highlighted the contribution of plant litter to microbial necromass to organic matter up to 1-m soil depth and elucidated the main factors regulating their long-term preservation.

The Effects of Dietary Chromium Supplementation along with Discontinuing a High-Fat Diet on the Microbial Enzymatic Activity and the Production of SCFAs in the Faeces of Rats

The present study assessed the changes in faecal microbial activity in obese Wistar rats fed high-fat or low-fat diets supplemented with various forms of chromium (picolinate or nanoparticles). The 18-week study was divided into two phases: an introductory period (9 weeks; obesity status induction via a high-fat diet) and an experimental period (9 weeks; maintained on a high-fat diet or switched to a low-fat diet and Cr supplementation). During the experimental period (10-18 weeks of feeding), samples of fresh faeces were collected on chosen days. The bacterial enzymatic activity and short-chain fatty acids (SCFAs) concentration were assessed to characterise the dynamism of the changes in faecal microbial metabolic activity under the applied dietary treatments. The results indicated that faecal microbial metabolic activity displayed several adaptation mechanisms in response to modifications in dietary conditions, and a beneficial outcome resulted from a pro-healthy dietary habit change, that is, switching from a high-fat to a low-fat diet. Dietary supplementation with chromium nanoparticles further modulated the aforementioned microbial activity, i.e., diminished the extracellular and total enzymatic activities, while the effect of chromium picolinate addition was negligible. Both the high-fat diet and the addition of chromium nanoparticles reduced SCFA concentrations and increased the faecal pH values.

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. To this end, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the diverse assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively smaller ones, is necessary and sufficient to recapitulate all of our experimental observations. In addition to pointing to a fundamental principle of community assembly, the divergence-complexity effect has important implications for microbiome engineering applications, as it can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions.

Bacillus subtilis extracellular protease production incurs a context-dependent cost

Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.

Periplasmic stress contributes to a trade-off between protein secretion and cell growth in Escherichia coli Nissle 1917

Maximizing protein secretion is an important target in the design of engineered living systems. In this paper, we characterize a trade-off between cell growth and per-cell protein secretion in the curli biofilm secretion system of Escherichia coli Nissle 1917. Initial characterization using 24-h continuous growth and protein production monitoring confirms decreased growth rates at high induction, leading to a local maximum in total protein production at intermediate induction. Propidium iodide (PI) staining at the endpoint indicates that cellular death is a dominant cause of growth reduction. Assaying variants with combinatorial constructs of inner and outer membrane secretion tags, we find that diminished growth at high production is specific to secretory variants associated with periplasmic stress mediated by outer membrane secretion and periplasmic accumulation of protein containing the outer membrane transport tag. RNA sequencing experiments indicate upregulation of known periplasmic stress response genes in the highly secreting variant, further implicating periplasmic stress in the growth-secretion trade-off. Overall, these results motivate additional strategies for optimizing total protein production and longevity of secretory engineered living systems Graphical Abstract.

Earthworms enhance the bioremediation of tris(2-butoxyethyl) phosphate-contaminated soil by releasing degrading microbes

The escalating awareness of the environmental risks posed by organophosphorus flame retardants (OPFRs), e.g., tris(2-butoxyethyl) phosphate (TBOEP), necessitates the development of effective approaches to mitigate their adverse ecological effects. However, research on the remediation of OPFR-contaminated soil remains limited. In this study, a strategy is proposed to enhance the microbial remediation of TBOEP-contaminated soil through the introduction of exotic earthworms (Eisenia fetida). The presence of earthworms led to a substantial increase in the 28-d removal rates of TBOEP at concentrations of 0.05, 0.5, and 5 mg/kg, with improvements of 32.3 ± 2.0%, 33.2 ± 1.3%, and 33.0 ± 5.6% compared to rates in the absence of earthworms, respectively. The underlying mechanisms for this enhancement include the earthworm-mediated enrichment of TBOEP-degrading bacteria, particularly Rhodococcus, Flavobacterium, and Pseudomonas, and the transfer of Rhodococcus from the earthworm gut to the soil, resulting in an increased relative abundance within the soil. Concurrently, the earthworms stimulated soil peroxidase activity, facilitating the oxidative degradation of TBOEP. Furthermore, the rise in dissolved organic matter content following earthworm treatment fostered the growth of degrading bacteria in the soil. Rhodococcus emerged as a dominant contributor to soil TBOEP removal, consuming humic-like compounds in dissolved organic matter. This investigation underscores the significance of gut microbes and offers valuable insights for the application of earthworm-based remediation strategies in OPFR-contaminated soil.

Variations in soil microbial community structure and extracellular enzymatic activities along a forest-wetland ecotone in high-latitude permafrost regions

Permafrost degradation by global warming is expected to alter the hydrological processes, which results in changes in vegetation species composition and gives rise to community succession. Ecotones are sensitive transition areas between ecosystem boundaries, attract particular interest due to their ecological importance and prompt responses to the environmental variables. However, the characteristics of soil microbial communities and extracellular enzymes along the forest-wetland ecotone in high-latitude permafrost region remain poorly understood. In this study, we evaluated the variations of soil bacterial and fungal community structures and soil extracellular enzymatic activities of 0-10 cm and 10-20 cm soil layers in five different wetland types along environmental gradients, including Larix gmelinii swamp (LY), Betula platyphylla swamp (BH), Alnus sibirica var. hirsute swamp (MCY), thicket swamp (GC), and tussock swamp (CC). The relative abundances of some dominant bacterial (Actinobacteria and Verrucomicrobia) and fungal (Ascomycota and Basidiomycota) phyla differed significantly among different wetlands, while bacterial and fungal alpha diversity was not strongly affected by soil depth. PCoA results showed that vegetation type, rather than soil depth explained more variation of soil microbial community structure. β-glucosidase and β-N-acetylglucosaminidase activities were significantly lower in GC and CC than in LY, BH, and MCY, while acid phosphatase activity was significantly higher in BH and GC than LY and CC. Altogether, the data suggest that soil moisture content (SMC) was the most important environmental factor contributing to the bacterial and fungal communities, while extracellular enzymatic activities were closely related to soil total organic carbon (TOC), nitrate nitrogen (NO 3 - -N ) and total phosphorus (TP).

Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism

Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.

Linking between soil properties, bacterial communities, enzyme activities, and soil organic carbon mineralization under ecological restoration in an alpine degraded grassland

Soil organic carbon (SOC) mineralization is affected by ecological restoration and plays an important role in the soil C cycle. However, the mechanism of ecological restoration on SOC mineralization remains unclear. Here, we collected soils from the degraded grassland that have undergone 14 years of ecological restoration by planting shrubs with Salix cupularis alone (SA) and, planting shrubs with Salix cupularis plus planting mixed grasses (SG), with the extremely degraded grassland underwent natural restoration as control (CK). We aimed to investigate the effect of ecological restoration on SOC mineralization at different soil depths, and to address the relative importance of biotic and abiotic drivers of SOC mineralization. Our results documented the statistically significant impacts of restoration mode and its interaction with soil depth on SOC mineralization. Compared with CK, the SA and SG increased the cumulative SOC mineralization but decreased C mineralization efficiency at the 0-20 and 20-40 cm soil depths. Random Forest analyses showed that soil depth, microbial biomass C (MBC), hot-water extractable organic C (HWEOC), and bacterial community composition were important indicators that predicted SOC mineralization. Structural equal modeling indicated that MBC, SOC, and C-cycling enzymes had positive effects on SOC mineralization. Bacterial community composition regulated SOC mineralization via controlling microbial biomass production and C-cycling enzyme activities. Overall, our study provides insights into soil biotic and abiotic factors in association with SOC mineralization, and contributes to understanding the effect and mechanism of ecological restoration on SOC mineralization in a degraded grassland in an alpine region.

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.

Eco-evolutionary modelling of microbial syntrophy indicates the robustness of cross-feeding over cross-facilitation

Syntrophic cooperation among prokaryotes is ubiquitous and diverse. It relies on unilateral or mutual aid that may be both catalytic and metabolic in nature. Hypotheses of eukaryotic origins claim that mitochondrial endosymbiosis emerged from mutually beneficial syntrophy of archaeal and bacterial partners. However, there are no other examples of prokaryotic syntrophy leading to endosymbiosis. One potential reason is that when externalized products become public goods, they incite social conflict due to selfish mutants that may undermine any mutualistic interactions. To rigorously evaluate these arguments, here we construct a general mathematical framework of the ecology and evolution of different types of syntrophic partnerships. We do so both in a general microbial and in a eukaryogenetic context. Studying the case where partners cross-feed on each other's self-inhibiting waste, we show that cooperative partnerships will eventually dominate over selfish mutants. By contrast, systems where producers actively secrete enzymes that cross-facilitate their partners' resource consumption are not robust against cheaters over evolutionary time. We conclude that cross-facilitation is unlikely to provide an adequate syntrophic origin for endosymbiosis, but that cross-feeding mutualisms may indeed have played that role.

Periplasmic stress contributes to a tradeoff between protein secretion and cell growth in E. Coli Nissile

Maximizing protein secretion is an important target in the design of engineered living systems. In this paper, we characterize a tradeoff between cell growth and per cell protein secretion in the curli biofilm secretion system of E Coli Nissile 1917. Initial characterization using 24-hour continuous growth and protein production monitoring confirms decreased growth rates at high induction leading to a local maximum in total protein production at intermediate induction. Propidium iodide staining at the endpoint indicates that cellular death is a dominant cause of growth reduction. Assaying variants with combinatorial constructs of inner and outer membrane secretion tags, we find that diminished growth at high production is specific to secretory variants associated with accumulation of protein containing the outer membrane transport tag in the periplasmic space. RNA sequencing experiments indicate upregulation of known periplasmic stress response genes in the highly secreting variant, further implicating periplasmic stress in the growth-secretion tradeoff. Overall, these results motivate additional strategies for optimizing total protein production and longevity of secretory engineered living systems.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation

In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.

Performance indicators, coccidia oocyst counts, plasma biochemical parameters and fermentation processes in the cecum of rabbits fed a diet with the addition of black cumin seed meal

The aim of this study was to determine the effects of dietary supplementation with black cumin seed meal on growth performance parameters, coccidia oocyst counts, plasma biochemical parameters and cecal fermentation processes in growing rabbits. A total of 40 male Californian rabbits at 35 days of age were divided into two feeding groups: Control (complete rabbit diet) and Black cumin (2% of the complete diet was replaced with black cumin seed meal). Dietary supplementation with black cumin did not affect growth performance parameters, but it reduced coccidia oocyst counts in the feces of 63-day-old rabbits. Increased liver weight and elevated plasma albumin levels were noted in these rabbits. A significant decrease in small intestinal digesta viscosity was also observed in rabbits fed a diet supplemented with black cumin seed meal. The above change suppressed the formation of putrefactive compounds, i.e. ammonia and branched short-chain fatty acids (SCFAs) in the cecum, but it did not decrease the production of major SCFAs, i.e. acetic, propionic and butyric acids. The current study demonstrated that the dietary addition of 2% black cumin seed meal exerted a modulatory effect on gastrointestinal function, but it did not compromise microbial enzyme activity or SCFA production in the cecum.

Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of ¹³ C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are associated with soil DNA content. Soil DNA yield is easy to measure and may be useful in predicting microbial community dynamics linked to soil carbon cycling. This article is protected by copyright. All rights reserved.

Identification and Characterization of a New Serratia proteamaculans Strain That Naturally Produces Significant Amount of Extracellular Laccase

Natural biodegradation processes hold promises for the conversion of agro-industrial lignocellulosic biomaterials into biofuels and fine chemicals through lignin-degrading enzymes. The high cost and low stability of these enzymes remain a significant challenge to economic lignocellulosic biomass conversion. Wood-degrading microorganisms are a great source for novel enzyme discoveries. In this study, the decomposed wood samples were screened, and a promising γ-proteobacterial strain that naturally secreted a significant amount of laccase enzyme was isolated and identified as Serratia proteamaculans AORB19 based on its phenotypic and genotypic characteristics. The laccase activities in culture medium of strain AORB19 were confirmed both qualitatively and quantitatively. Significant cultural parameters for laccase production under submerged conditions were identified following a one-factor-at-a-time (OFAT) methodology: temperature 30°C, pH 9, yeast extract (2 g/l), Li+, Cu2+, Ca2+, and Mn2+ (0.5 mM), and acetone (5%). Under the selected conditions, a 6-fold increase (73.3 U/L) in laccase production was achieved when compared with the initial culturing conditions (12.18 U/L). Furthermore, laccase production was enhanced under alkaline and mesophilic growth conditions in the presence of metal ions and organic solvents. The results of the study suggest the promising potential of the identified strain and its enzymes in the valorization of lignocellulosic wastes. Further optimization of culturing conditions to enhance the AORB19 strain laccase secretion, identification and characterization of the purified enzyme, and heterologous expression of the specific enzyme may lead to practical industrial and environmental applications.

Biotechnological formation of dairy flavor inducing δ-lactones from vegetable oil

Agroscope Culture Collection was screened to identify bacterial strains effective in production of dairy flavor inducing lactones using grapeseed oil as a substrate. Lentilactobacillus parafarraginis FAM-1079, Lactococcus lactis subsp. lactis FAM-17918, and L. lactis subsp. lactis biovar diacetylactis FAM-22003 showed the most efficient formation of targeted δ-lactones. The application of sublethal heat stress significantly increased target lactone production. The most profound improvement was for L. lactis subsp. lactis biovar diacetylactis where δ-octadecalactone generation was improved by factor of 9. The pre-fermentation step as well as growth phase in which bacteria are harvested did not have a significant impact on lactones yield. The lactone production process from vegetable oil developed in this study offers a new way of developing a natural flavor ingredient for incorporation into plant-based products.

A Game Theoretic Analysis of the Dual Function of Antibiotics

There are two major views toward the role of antibiotics in microbial social interactions. The classical view is that antibiotics serve as weapons, produced by a bacterial species, at a significant cost, to inhibit the growth of its competitors. This view is supported by observations that antibiotics are usually upregulated by stress responses that infer the intensity of ecological competition, such as nutrient limitation and cellular damage, which point out to a competitive role for antibiotics. The other ecological function frequently assigned to antibiotics is that they serve as signaling molecules which regulate the collective behavior of a microbial community. Here, we investigate the conditions at which a weapon can serve as a signal in the context of microbial competition. We propose that an antibiotic will serve as a signal whenever a potential alteration of the growth behavior of the signal receiver, in response to a subinhibitory concentration (SIC) of the antibiotic, reduces the competitive pressure on the signal producer. This in turn would lead to avoiding triggering the stress mechanisms of the signal producer responsible for further antibiotics production. We show using individual-based modeling that this reduction of competitive pressure on the signal producer can happen through two main classes of responses by the signal recipient: competition tolerance, where the recipient reduces its competitive impact on the signal producer by switching to a low growth rate/ high yield strategy, and niche segregation, where the recipient reduces the competitive pressure on the signal producer by reducing their niche overlap. Our hypothesis proposes that antibiotics serve as signals out of their original function as weapons in order to reduce the chances of engaging in fights that would be costly to both the antibiotic producer as well as to its competitors.

Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q₁₀ and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (V_max) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. V_max and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q₁₀ and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.

Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria

Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how microbiomes and their functions respond to resources and stress across space, time, and diverse ecosystems. We demonstrate the potential of this framework by applying it to the microbiomes hosted by the carnivorous pitcher plant Sarracenia purpurea, which have clear successional trajectories and are distributed across a broad climatic gradient.

Phenotypic plasticity of fungal traits in response to moisture and temperature

Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4-50% water holding capacity) and at five temperatures (ranging from 4-36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.

Investigations of the maintenance system of the Konik Polski horse and its effects on fecal microbiota activity during the winter and summer seasons

Gastrointestinal microbiota play a key role in the nutrients digestion and hence maintaining animal health and welfare. The diet offered to the animals in captivity may differ considerably from that on natural pastures. In a stabled maintenance system, horses have a limited choice of habitat and feed. Time spend for feeding is relevant for equine welfare because the reduction of the time devoted for foraging may be responsible for inducing gastric inflammation and ulceration. Therefore, in the present study, it was hypothesized that fecal bacterial fermentative processes differ between free-roaming and stabled Konik Polski Horses (KPHs) with respect to microbial enzymatic activity, and thus the fecal concentration of short-chain fatty acids (SCFA), which can be further utilized for assessing the feeding behavior and welfare in free-roaming versus stabled horses. The SCFA concentration and profile, as well as the extracellular and intracellular activities of selected bacterial enzymes, were characterized in horse feces collected during the winter and summer feeding seasons. The results showed higher enzymatic activity and SCFA production in the feces excreted by free-roaming versus stabled horses, especially during summer. An increase in pasture plant diversity may be beneficial for the gastrointestinal microbiota and hence for maintaining health and welfare.

Soil chemical properties rather than the abundance of active and potentially active microorganisms control soil enzyme kinetics

Soil enzymes secreted by microorganisms play a critical role in nutrient cycling, soil structure maintenance, and crop production. However, understanding of the linkage between soil enzyme kinetics and microbial metabolism and active microbial communities is remarkably limited. In this study, we measured the kinetics of three hydrolase enzymes, active microbial abundance and substrate-induced respiration (SIR) from 21 farmlands differing in their fertilities collected from the Loess Plateau, China. Results showed the high fertility soils had higher total organic carbon (TOC) and nutrient contents, potential microbial activity, the colony-forming units (CFU) of actinomycetes, and values of enzyme V_max and K_m than those of low fertility soils. We also observed that the CFU of fungi and other bacterial groups did not change with soil fertility status. Soil chemical properties explained 74.0% of the variance in V_max and 28.3% of the variance in K_m, respectively. Whereas, the abundance of main microbial groups and fungi/bacteria ratio only explained 10.2% and 7% of the variance of V_max and K_m, respectively. The interactive effect of soil properties and microbial community could explain 20.2% of the variance in K_m. Our results suggest that the substrate availability would mainly drive enzyme kinetics compared to the abundance of active/potentially active microbes in the farmland soils.

Influence of Supplementation of Lactoferrin, Melittin and Cecropin A to Rat Diet on Changes in Faecal Ammonia Concentrations, Short-Chain Fatty Acid Concentrations and Activities of Bacterial Enzymes

Simple Summary

In the present study conducted on Wistar laboratory rats, the effects of two selected insect antimicrobial peptides (AMPs), melittin and cecropin A, were investigated and compared to those attributed to well-known antibacterial action of lactoferrin. It was hypothesised that the dietary presence of lactoferrin, melittin or cecropin A strongly affects the rat large gut microbial activity at the time of protein/peptide administration and the durability of the effects may differ after their withdrawal from a diet. The experiment was conducted on living animals (without their euthanasia) and the dynamics of changes in pH, microbial enzyme activity, ammonia and short-chain fatty acids concentrations were investigated in the faeces during and after the dietary treatments with lactoferrin, melittin or cecropin A. The results suggested that the faecal intensity of microbial fermentation processes in rats was quickly reduced upon dietary addition of two AMPs and lactoferrin after two days of treatment, on average. The strongest suppression effect was observed on the 5th day of treatment and persisted on days 5–8. The changes caused by the supplemented lactoferrin and AMPs were reversible after 15 days, i.e., 10 days after the withdrawal of lactoferrin, melittin and cecropin A from the diet.

Abstract

We hypothesised that the dietary addition of the bioactive antimicrobial protein lactoferrin (LF) and peptides melittin (MT) or cecropin A (CR) at a dosage of 100 mg/kg to the diet of Wistar rats would result in strong modulatory effects on faecal microbial enzymatic activity, short-chain fatty acid and ammonia concentrations. To date, the changes in bacterial extracellular and intracellular enzymatic activities upon addition of dietary AMPs have not yet been studied. This experiment lasted 15 days; during the first 5 day period, the rats were fed the control diet (S) and diets supplemented with LF, MT or CR. On days 6–15, all rats were fed the control S diet. The faecal fermentation processes were substantially stopped after two days of treatment, on average, in all rats receiving LF and two AMPs. The deepest suppression effect was observed on the last day of treatment (day 5) and persisted through days 5–8. The highest decreases in faecal bacterial β-glucosidase and β-glucuronidase activities as well as in SCFA and ammonia concentrations were observed in the rats fed the CR diet. Only in the CR animals did the mechanism of suppressed microbial fermentation involve diminished enzyme release from bacterial cells to the digesta.

Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.

Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams

Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand’s Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.

Community lifespan, niche expansion and the evolution of interspecific cooperation

Microbes live in dense and diverse communities where they deploy many traits that promote the growth and survival of neighbouring species, all the while also competing for shared resources. Because microbial communities are highly dynamic, the costs and benefits of species interactions change over the growth cycle of a community. How mutualistic interactions evolve under such demographic and ecological conditions is still poorly understood. Here, we develop an eco-evolutionary model to explore how different forms of helping with distinct fitness effects (rate-enhancing and yield-enhancing) affect the multiple phases of community growth, and its consequences for the evolution of mutualisms. We specifically focus on a form of yield-enhancing trait in which cooperation augments the common pool of resources, termed niche expansion. We show that although mutualisms in which cooperation increases partners growth rate are generally favoured at early stages of community growth, niche expansion can evolve at later stages where densities are high. Further, we find that niche expansion can promote the evolution of reproductive restraint, in which a focal species adaptively reduces its own growth rate to increase the density of partner species. Our findings suggest that yield-enhancing mutualisms are more prevalent in stable habitats with a constant supply of resources, and where populations typically live at high densities. In general, our findings highlight the need to integrate different components of population growth in the analysis of mutualisms to understand the composition and function of microbial communities.

Effects of nitrogen fertilization and bioenergy crop species on central tendency and spatial heterogeneity of soil glycosidase activities

Extracellular glycosidases in soil, produced by microorganisms, act as major agents for decomposing labile soil organic carbon (e.g., cellulose). Soil extracellular glycosidases are significantly affected by nitrogen (N) fertilization but fertilization effects on spatial distributions of soil glycosidases have not been well addressed. Whether the effects of N fertilization vary with bioenergy crop species also remains unclear. Based on a 3-year fertilization experiment in Middle Tennessee, USA, a total of 288 soil samples in topsoil (0–15 cm) were collected from two 15 m² plots under three fertilization treatments in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) using a spatially explicit design. Four glycosidases, α-glucosidase (AG), β-glucosidase (BG), β-xylosidase (BX), cellobiohydrolase (CBH), and their sum associated with C acquisition (C_acq) were quantified. The three fertilization treatments were no N input (NN), low N input (LN: 84 kg N ha⁻¹ year⁻¹ in urea) and high N input (HN: 168 kg N ha⁻¹ year⁻¹ in urea). The descriptive and geostatistical approaches were used to evaluate their central tendency and spatial heterogeneity. Results showed significant interactive effects of N fertilization and crop type on BX such that LN and HN significantly enhanced BX by 14% and 44% in SG, respectively. The significant effect of crop type was identified and glycosidase activities were 15–39% higher in GG than those in SG except AG. Within-plot variances of glycosidases appeared higher in SG than GG but little differed with N fertilization due to large plot-plot variation. Spatial patterns were generally more evident in LN or HN plots than NN plots for BG in SG and CBH in GG. This study suggested that N fertilization elevated central tendency and spatial heterogeneity of glycosidase activities in surficial soil horizons and these effects however varied with crop and enzyme types. Future studies need to focus on specific enzyme in certain bioenergy cropland soil when N fertilization effect is evaluated.

Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition

Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.

Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources

The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli, ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis, Flavobacterium terrae, Niastella vici, and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.