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Conversion from agriculture to grassland builds soil organic matter on decadal timescales.

Soil organic matter (SOM) often increases when agricultural fields are converted to perennial vegetation, yet decadal scale rates and the mechanisms that underlie SOM accumulation are not clear. We measured SOM accumulation and changes in soil properties on a replicated chronosequence of former agricultural fields in the midwestern United States that spanned 40 years after perennial-grassland establishment. Over this time period, soil organic carbon (SOC) in the top 10 cm of soil accumulated at a constant rate of 62.0 g x m(-2) x yr(-1), regardless of whether the vegetation type was dominated by C3 or C4 grasses. At this rate, SOC contents will be equivalent to unplowed native prairie sites within 55-75 years after cultivation ceased. Both labile (short turnover time) and recalcitrant (long turnover time) carbon pools increased linearly for 40 years, with recalcitrant pools increasing more rapidly than expected. This result was consistent across several different methods of measuring labile SOC. A model that investigates the mechanisms of SOM formation suggests that rapid formation of stable carbon resulted from biochemically resistant microbial products and plant material. Former agricultural soils of the Great Plains may function as carbon sinks for less than a century, although much of the carbon stored is stable.

Agriculture↗

Why do many ruminal bacteria die and lyse so quickly?

Studies using 15N have indicated that as much as 50% of the microbial mass turns over before N passes to the lower gut, and this N recycling significantly decreases the availability of microbial protein. Protozoa digest bacteria and smaller protozoa, but bacterial protein can turn over even if protozoa are not present. Fibrobacter succinogenes cultures lyse even when they are growing, and the lysis rate is independent of growth rate. When extracellular sugar is depleted, F. succinogenes secretes an extracellular proteinase that inactivates the autolysins. This method of autolytic regulation decreases the turnover of stationary cells. Bacteriophage and anaeroplasma can cause lysogeny, but, as yet, there is little proof that these processes are important determinants of bacterial turnover in vivo. Dietary manipulations (e.g., salt feeding and particle size reduction) that increase liquid and solid dilution rates can increase bacterial flow by decreasing bacterial residence time and turnover. Some dead ruminal bacteria are able to maintain their cellular integrity, and the ratio of dead to live cells in ruminal fluid may be as great as 10:1. Bacterial survival appears to be at least partially explained by the method of sugar transport. When bacteria rely solely on mechanisms of ion-coupled sugar symport, an energized membrane is necessary for the reinitiation of growth. If group translocation (phosphotransferase system) is the mechanisms of transport, uptake can be driven by phosphoenolpyruvate, and an energized membrane and the storage of intracellular reserve materials are not an absolute criteria for survival. In some cases, N deprivation accelerates death. When Prevotella ruminicola was limited for N under conditions of excess energy, methylglyoxal production caused a rapid decrease in viability. The impact of bacterial death in the rumen is not clear-cut. If the rate of fermentation is zero-order with respect to cell concentration (substrate-limited), cell death would have little impact on digestion.

Animals↗

Relaxin modulates synthesis and secretion of procollagenase and collagen by human dermal fibroblasts.

Relaxin is believed to play a role in connective tissue remodeling during pregnancy (Bell, R.J., Eddie, L. W., Lester, A. R., Wood, E. C., Johnston, P.D., and Niall, H. D. (1987) Obstet. Gynecol. 69, 585-589; MacLennan, A. H. (1983) Clin. Reprod. Fertil. 2, 77-95). In the present study, normal human fibroblasts exposed to concentrations of a synthetic bioactive relaxin peptide from 0.1 to 10 ng/ml synthesized and secreted the metalloproteinase procollagenase, which was immunoprecipitable as a doublet of 52 and 57 kDa by a monoclonal antibody to human collagenase. The stimulation in procollagenase protein expression was reflected in an elevation in procollagenase mRNA levels. Media conditioned for 48 h by relaxin-treated fibroblasts (0.1 ng/ml) contained 1.7 units/ml activatable collagenase compared with 0.2 units/ml by untreated fibroblasts. In addition, relaxin caused a modest decrease in the levels of tissue inhibitor of metalloproteinases, as detected by reverse zymography and Northern analysis. Relaxin was also a potent modulator of the collagen secretory phenotype of these fibroblasts. Relaxin at 100 ng/ml down-regulated collagen secretion by 40%. When fibroblasts were treated simultaneously with cytokines such as transforming growth factor beta or interleukin 1 beta, which stimulated collagen synthesis to at least 9-fold of basal levels, relaxin at 100 ng/ml was able to down-regulate collagen expression by up to 88%. This decrease was reflected by changes at the mRNA level. These results indicate that relaxin can cause significant collagen turnover both by stimulating collagenase expression and by down-modulating collagen synthesis and secretion.

Cells, Cultured↗

IKKalpha limits macrophage NF-kappaB activation and contributes to the resolution of inflammation.

Inflammation and innate immunity involve signalling pathways leading to the production of inflammatory mediators. Usually such responses are self-limiting, but aberrant resolution of inflammation results in chronic diseases. Much attention has focused on pro-inflammatory signalling but little is known about the mechanisms that resolve inflammation. The IkappaB kinase (IKK) complex contains two catalytic subunits, IKKalpha and IKKbeta, and controls the activation of NF-kappaB transcription factors, which play a pivotal role in inflammation. Ample evidence indicates that IKKbeta mediates NF-kappaB activation in response to pro-inflammatory cytokines and microbial products. IKKalpha regulates an alternative pathway important for lymphoid organogenesis, but the role of IKKalpha in inflammation is unknown. Here we describe a new role for IKKalpha in the negative regulation of macrophage activation and inflammation. IKKalpha contributes to suppression of NF-kappaB activity by accelerating both the turnover of the NF-kappaB subunits RelA and c-Rel, and their removal from pro-inflammatory gene promoters. Inactivation of IKKalpha in mice enhances inflammation and bacterial clearance. Hence, the two IKK catalytic subunits have evolved opposing but complimentary roles needed for the intricate control of inflammation and innate immunity.

Animals↗

Mucosal morphology, bacteriology, and absorption in intra-abdominal ileostomy reservoir.

Six patients who had undergone proctocolectomy and been provided with intra-abdominal ileostomy reservoirs were studied in intervals during the 24 postoperative months. The studies included the mucosal morphology, bacteriology, and the local absorption in the reservoir. The results showed that the mucous membrane of the terminal ileal segment used for construction of the reservoir underwent morphological changes characterized by an increased cell turnover and a shortening of the villi. These changes in morphological structure took place rather promptly after construction of the reservoir. No indications for a continuously progressing process could be found. The brushborder was intact and no cellular lesions were discovered. Soon after construction the reservoir was inhabited by a microbial flora which held an intermediate position between the flora of effluent from conventional ileostomies and normal faeces. The flora remained rather stable in the reservoir. In spite of the new microbial ecology and the morphological changes, the reservoir mucous membrane did retain absorptive capacity for D-xylose and phenylalanine.

Biopsy↗

Children with recurrent episodes of acute otitis media: the effect of local administration of immunoglobulin G on acute otitis media, colonization and turnover of non-encapsulated Haemophilus influenzae in the nasopharynx.

In most children with recurrent episodes of acute otitis media (AOM), tube treatment is successful, but there are those who nevertheless suffer from middle ear infections. The aim of the present study was to ascertain whether local administration of immunoglobulin could reduce the number of episodes of otorrhoea in otitis-prone infants <2 years old who were treated with tubes, or whether it could affect the nasopharyngeal colonization and turnover of bacterial pathogens in the nasopharynx. IgG or placebo were also administered intranasally daily for 6 months to 50 infants, randomized in a double-blind study. An arbitrarily primed polymerase chain reaction (AP-PCR) was used to characterize the different isolates of NTHI (non-encapsulated, non-typable Haemophilus influenzae). Three infants in the IgG group and six infants in the control group suffered from > or =3 episodes of acute otitis media. No effect on the nasopharyngeal colonization or the turnover of non-encapsulated H. influenzae in the nasopharynx could be detected in either group.

Acute Disease↗

Higher abundance of bacteria than of viruses in deep Mediterranean sediments.

The interactions between viral abundance and bacterial density, biomass, and production were investigated along a longitudinal transect consisting of nine deep-sea stations encompassing the entire Mediterranean basin. The numbers of viruses were very low (range, 3.6 x 10(7) to 12.0 x 10(7) viruses g(-1)) and decreased eastward. The virus-to-bacterium ratio was always < 1.0, indicating that the deep-sea sediments of the Mediterranean Sea are the first example of a marine ecosystem not numerically dominated by viruses. The lowest virus numbers were found where the lowest bacterial metabolism and turnover rates and the largest cell size were observed, suggesting that bacterial doubling time might play an important role in benthic virus development.

Bacteria↗

Transcriptional activation of fibroblast collagenase gene expression by a novel lymphokine, leukoregulin.

Leukoregulin (LR) is a novel T-cell derived cytokine with unique anti-tumor properties. We have recently demonstrated that LR is also able to modulate the biosynthetic repertoire of normal human skin fibroblasts in culture (Mauviel, A., Rédini, F., Hartmann, D.J., Pujol, J.-P., and Evans, C.H. (1991) J. Cell Biol. 113, 1455-1462). In this study, we have examined in detail the effects of LR on collagenase gene expression in human skin fibroblast cultures. The results indicated time- and dose-dependent induction of collagenase mRNA steady-state levels, the maximum elevation being approximately 35-fold. In contrast, the mRNA levels for tissue inhibitor of metalloproteases remained unchanged in the same RNA preparations. The enhancement of collagenase mRNA levels was shown to be dependent on protein synthesis, and it could be counteracted by dexamethasone or all-trans-retinoic acid. Transient transfections of cultured fibroblasts with a human collagenase promoter/reporter gene construct indicated up-regulation of the promoter activity, which could be blocked by dexamethasone and all-trans-retinoic acid. The observation suggested regulation at the transcriptional level of collagenase gene expression. LR was also shown to induce the mRNA levels for junB, suggesting possible involvement of the AP-1 complex in the regulation. The ability of LR to selectively induce collagenase gene expression in skin fibroblasts suggests that this cytokine may significantly contribute to the degradation of the extracellular matrix in physiological situations, such as tissue development and repair, and in diseases characterized by excessive degradation and turnover of collagen.

3T3 Cells↗

The kinetic mechanism of kanamycin acetyltransferase derived from the use of alternative antibiotics and coenzymes.

Kinetic data for the 6'-aminoglycoside-modifying enzyme, AAC(6')-4, also named kanamycin acetyltransferase, have been collected for six aminoglycoside antibiotics (amikacin, gentamicin C1a, kanamycin A, neomycin B, sisomicin, and tobramycin) and three coenzymes (acetyl-CoA, n-propionyl-CoA, and n-butyryl-CoA). The initial velocity pattern using acetyl-CoA favors a ping-pong kinetic mechanism (Kia = -0.34 +/- 0.34 microM), but the pattern using n-propionyl-CoA supports a sequential one (Kia = 2.7 +/- 0.8 microM). Kinetic analyses using alternative substrates confirm the sequential mechanism and, moreover, clearly identify a random order of addition of antibiotic and coenzyme because V/K values of antibiotics varied 40-fold as the identity of the coenzyme was changed and V/K values of coenzyme varied 13-fold as the identity of the antibiotic was changed. One or both sets of values would have remained unchanged if the mechanism were either ordered sequential or ping-pong. Combining these results with structure-activity data which argue for a rapid rate of release of substrates and products relative to the rate of enzymatic turnover (Radika, K., and Northrop, D. B. (1984) Biochemistry 25, in press) establishes the kinetic mechanism as rapid equilibrium random sequential.

Acetyltransferases↗

Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.

Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.

Animals↗

The deep subsurface biosphere is alive and well.

For the first time, metabolically active bacterial cells have recently been quantified in deep marine sediments. In contrast to previous total cell counts that do not differentiate between active cells and inactive or dormant cells, these quantifications using oligonucleotide hybridization probes target active cells and their ribosomal (r)RNA. They demonstrate a sizable, active bacterial subsurface biosphere, and allow realistic estimates of cell-specific respiration rates and turnover times for living bacteria in this global extreme habitat. In situ activities and physiologies of these active subsurface microbiota emerge as high-priority research areas.

Bacterial Physiological Phenomena↗

Metalloproteinases are not involved in the phagocytosis of collagen fibrils by fibroblasts.

The effect of various metalloproteinase-inhibiting compounds on collagen phagocytosis by fibroblasts was studied in cultured periosteal tissue. Evidence is presented indicating that neither anti-collagenase nor anti-stromelysin interfere with the uptake of collagen fibrils from the extracellular space and their intracellular digestion. Similar results were obtained with tissue inhibitor of metalloproteinases (TIMP). In the presence of the proteinase inhibitor leupeptin, a compound which strongly inhibits the intracellular degradation of phagocytosed collagen, a time-dependent increase in the amount of internalized collagen was found. This increase proved to be similar in explants treated as well as in those not treated with the metalloproteinase-inhibiting compounds. It is concluded that enzymes, such as collagenase and stromelysin, do not play a crucial role in the phagocytosis and intracellular digestion of collagen fibrils by fibroblasts. If these enzymes are involved it must be prior to these events. Based on the morphometric data the intralysosomal degradation time of collagen was calculated to be about 30 minutes. A comparison with findings in the literature on collagen metabolism in the periodontal ligament of the rat molar suggests that all collagen degraded may pass through the phagolysome pathway during physiological turnover and remodelling.

Animals↗

Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria.

Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25-22 yr, comparable to surface sediments.

Archaea↗

The immune response to dietary antigens and its influence on disease susceptibility in farm animals.

Transient hypersensitivity reactions of the intestinal immune system to dietary antigens result in increases in enterocyte turnover and villous atrophy. These changes occur in the intestine of the post weaned piglet and precede the proliferation of E. coli and the development of post-weaning diarrhea. We therefore postulated that a transient cell mediated immune response to dietary antigens may increase susceptibility to disease. The interaction of dietary and microbial antigens upon the gut immune system has been investigated in mice and pigs and it has been shown that both exert powerful regulatory effects upon each other.

Adjuvants, Immunologic↗

Compost microbiomes as reservoirs of cellulolytic microorganisms for cellulosic textile degradation.

Cellulosic textiles, constituting over 30% of global fibre production, are biodegradable but remain challenging to recycle at scale owing to their high crystallinity, chemical finishes, and heterogeneous waste streams. Although microorganisms drive cellulose turnover in natural ecosystems, their potential for transforming anthropogenic cellulosic waste remains largely unexplored. In this study, composting was evaluated both as a sustainable approach to textile biodegradation and a reservoir of cellulolytic microorganisms with biotechnological potential. Biodegradation assays of cotton and lyocell were integrated with shotgun metagenomics and targeted cultivation to identify microbial taxa and enzymes involved in cellulose degradation. Composting trials showed that degradation was strongly influenced by both composting system and fibre composition. Community composting achieved near-complete textile disintegration, while shredded textiles exhibited the highest degradation rates, reaching up to 97%. Shotgun metagenomic revealed a bacterial-dominated community enriched in Actinomycetota and Bacillota and characterised by an abundance of glycoside hydrolases. Culture-based screening recovered 62 microbial isolates, of which Neurospora and Aspergillus exhibited the highest cellulolytic activity (>60%). In vitro assays further showed that cotton was more readily degraded than lyocell, with several isolates achieving&#xa0;>70% mass loss. Metagenomic approach revealed a predominantly bacterial composting community at the sampled stage, whereas cultivation preferentially recovered fungi that, despite their low relative abundance in situ, exhibited strong cellulolytic potential. These findings highlight the potential of composting as a sustainable end-of-life strategy for cellulosic textiles and identify compost microbiomes as valuable reservoirs of cellulolytic microorganisms for the development of sustainable bioprocesses for textile waste treatment.

Cellulose↗

Bio-available amino acids and mineral nitrogen forms in soil of moderately mown and abandoned mountain meadows.

The abandonment of traditional mowing methods of mountain meadows in the Czech Republic at the end of the last century has resulted in secondary re-colonization of these areas. Altered accumulation of plant biomass resulted in a deceleration of N turnover. A mountain meadow may be regarded as a N-limited ecosystem in which plant nutrition is dependent on direct uptake of soil amino acids. The composition and distribution of ammonium ions, nitrate ions and the 16 bio-available proteinaceous amino acids were investigated in the top 7 cm of the Ah horizon of a Gleyic Luvisol in a long-term moderately mown meadow and an eleven year old, abandoned or uncut meadow. Ammonium N has a dominant role in both ecosystems. The moderately mown meadow showed accelerated N-turnover and higher net ammonization. The plant community showed a dependence on this form. Plant utilization of nitrates and amino acids appeared to be negligible. The uncut or abandoned meadow showed net ammonization from May (start of the experiment) through August, after which plant N-uptake consisted only of amino acids due to microbial immobilization. The release of bio-available nitrogen from spring until the beginning of summer in the Ah horizon was too low to explain total plant N-uptake. Glutamic acid, arginine and aspartic acids had the highest concentrations of any of the amino acids analyzed.

Agriculture↗

Human mesangial cells secrete a GBM-degrading neutral proteinase and a specific inhibitor.

The factors operative during normal and disease states which govern the degradation of the glomerular extracellular matrix (ECM, glomerular basement membrane and mesangial matrix) remain poorly understood. These structures consist primarily of types IV and V collagen, which are highly resistant to the action of classical interstitial collagenases. Here we report that an intrinsic glomerular cell type, the human mesangial cell, secretes: 1) a neutral proteinase with specific activity against type IV basement membrane collagen and, 2) an inhibitory protein with the characteristics of the tissue inhibitor of metalloproteinases (TIMP). The purified enzyme has a neutral pH optimum, consists of a basic (pI 8.4) protein doublet with molecular weight of 66 and 68 kilodaltons, and is inhibited by calcium and zinc chelators. The enzyme degrades both soluble and basement membrane type IV collagen, but does not specifically degrade types I or V collagen or casein. Immunohistochemistry of cultured cells demonstrated homogeneous staining for the neutral proteinase antigen, while the TIMP antigen was detected in fewer than one-third of cultured cells. These findings suggest that the synthesis of these proteins may be independently regulated. The secretion of these factors may play an important role in the turnover of the glomerular ECM under basal or pathologic conditions.

Basement Membrane↗

Effect of zinc deficiency on bone collagenase and collagen turnover.

The effect of zinc deficiency on bone collagenase activity and collagen turnover was studied in the chick. Zinc deficiency symptoms, evident after 8 days on the low zinc diet, included tibia deformities and decreased alkaline phosphatase. Bone collagen metabolism was markedly altered, with a significant reduction in collagen synthesis and turnover. Half-turnover time for tibia collagen was 13 days in the control and 35 days in the zinc-deficient chicks. Tibia collagenase activity was reduced by 40-80% in the zinc-deficient as compared to the control chicks. Heparin markedly increased collagenase activity in the zinc-deficient tibias elevating activity to control levels. But commercially available heparin was found high in zinc content which may explain this effect entirely. These data show that zinc deficiency decreases bone collagen turnover and probably accounts for the leg deformities seen in zinc-deficient chicks.

Alkaline Phosphatase↗