The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile.

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping.

Quickly identifying and characterizing isolates from extreme environments is currently challenging while very important to explore the Earth's biodiversity. As these isolates may, in principle, be distantly related to known species, techniques are needed to reliably identify the branch of life to which they belong. Proteotyping these environmental isolates by tandem mass spectrometry offers a rapid and cost-effective option for their identification using their peptide profiles. In this study, we document the first high-throughput proteotyping approach for environmental extremophilic and halophilic isolates. Microorganisms were isolated from samples originating from high-altitude Andean lakes (3700-4300 m a.s.l.) in the Chilean Altiplano, which represent environments on Earth that resemble conditions on other planets. A total of 66 microorganisms were cultivated and identified by proteotyping and 16S rRNA gene amplicon sequencing. Both the approaches revealed the same genus identification for all isolates except for three isolates possibly representing not yet taxonomically characterized organisms based on their peptidomes. Proteotyping was able to indicate the presence of two potentially new genera from the families of Paracoccaceae and Chromatiaceae/Alteromonadaceae, which have been overlooked by 16S rRNA amplicon sequencing approach only. The paper highlights that proteotyping has the potential to discover undescribed microorganisms from extreme environments.

Diversity of Root-Associated Fungi of the Terrestrial Orchids Gavilea lutea and Chloraea collicensis in a Temperate Forest Soil of South-Central Chile.

The diversity of orchid mycorrhizal fungi (OMF) and other beneficial root-associated fungi in temperate forests has scarcely been examined. This study aimed to analyze the diversity of mycorrhizal and rhizosphere-associated fungal communities in the terrestrial orchids Gavilea lutea and Chloraea collicensis growing in high-orchid-population-density areas in the piedmont of the Andes Cordillera with native forest (Nothofagus-Araucaria) and Coastal Cordillera with an exotic plantation (Pinus-Eucalyptus) in south-central Chile. We focused on rhizosphere-inhabiting and peloton-associated OMF in a native forest (Andes Cordillera) and a mixed forest (Coastal Cordillera). The native terrestrial orchids G. lutea and C. collicensis were localized, mycorrhizal root segments were taken to isolate peloton-associated OMF, and rhizosphere soil was taken to perform the metabarcoding approach. The results revealed that Basidiomycota and Ascomycota were the main rhizosphere-inhabiting fungal phyla, showing significant differences in the composition of fungal communities in both sites. Sebacina was the most-abundant OMF genera in the rhizosphere of G. lutea growing in the native forest soil. In contrast, Thanatephorus was the most abundant mycorrhizal taxa growing in the rhizosphere of orchids from the Coastal Cordillera. Besides, other OMF genera such as Inocybe, Tomentella, and Mycena were detected. The diversity of OMF in pelotons differed, being mainly related to Ceratobasidium sp. and Tulasnella sp. These results provide evidence of differences in OMF from pelotons and the rhizosphere soil in G. lutea growing in the Andes Cordillera and a selection of microbial communities in the rhizosphere of C. collicensis in the Coastal Cordillera. This raises questions about the efficiency of propagation strategies based only on mycorrhizal fungi obtained by culture-dependent methods, especially in orchids that depend on non-culturable taxa for seed germination and plantlet development.

Biological Crusts to Increase Soil Carbon Sequestration: New Challenges in a New Environment.

The major priority of research in the present day is to conserve the environment by reducing GHG emissions. A proposed solution by an expert panel from 195 countries meeting at COP 21 was to increase global SOC stocks by 0.4% year-1 to compensate for GHG emissions, the '4 per 1000' agreement. In this context, the application of biocrusts is a promising framework with which to increase SOC and other soil functions in the soil-plant continuum. Despite the importance of biocrusts, their application to agriculture is limited due to: (1) competition with native microbiota, (2) difficulties in applying them on a large scale, (3) a lack of studies based on carbon (C) balance and suitable for model parameterization, and (4) a lack of studies evaluating the contribution of biocrust weathering to increase C sequestration. Considering these four challenges, we propose three perspectives for biocrust application: (1) natural microbiome engineering by a host plant, using biocrusts; (2) quantifying the contribution of biocrusts to C sequestration in soils; and (3) enhanced biocrust weathering to improve C sequestration. Thus, we focus this opinion article on new challenges by using the specialized microbiome of biocrusts to be applied in a new environment to counteract the negative effects of climate change.

Manganese-Oxidizing Antarctic Bacteria (Mn-Oxb) Release Reactive Oxygen Species (ROS) as Secondary Mn(II) Oxidation Mechanisms to Avoid Toxicity.

Manganese (Mn) oxidation is performed through oxidative Mn-oxidizing bacteria (MnOxb) as the main bio-weathering mechanism for Mn(III/IV) deposits during soil formation. However, with an increase in temperature, the respiration rate also increases, producing Reactive Oxygen Species (ROS) as by-products, which are harmful to microbial cells. We hypothesize that bacterial ROS oxidize Mn(II) to Mn(III/IV) as a secondary non-enzymatic temperature-dependent mechanism for cell protection. Fourteen MnOxb were isolated from Antarctic soils under the global warming effect, and peroxidase (PO) activity, ROS, and Mn(III/IV) production were evaluated for 120 h of incubation at 4 °C, 15 °C, and 30 °C. ROS contributions to Mn oxidation were evaluated in Arthrobacter oxydans under antioxidant (Trolox) and ROS-stimulated (menadione) conditions. The Mn(III/IV) concentration increased with temperature and positively correlated with ROS production. ROS scavenging with Trolox depleted the Mn oxidation, and ROS-stimulant increased the Mn precipitation in A. oxydans. Increasing the Mn(II) concentration caused a reduction in the membrane potential and bacterial viability, which resulted in Mn precipitation on the bacteria surface. In conclusion, bacterial ROS production serves as a complementary non-enzymatic temperature-dependent mechanism for Mn(II) oxidation as a response in warming environments.

Soil Redox Controls CO2, CH4 and N2O Efflux from White-Rot Fungi in Temperate Forest Ecosystems.

Microaerophilic white-rot fungi (WRF) are impacted by oxygen depletion because of fluctuating redox occurrence in southern temperate forest soils of Chile (1500-5000 mm year-1). How these conditions influence WRF survival has been scarcely examined. We explored the contributions of WRF to greenhouse gas (GHG) emissions of N2O and CH4 and soil organic C oxidation (CO2) in five sterilized and inoculated forest soils derived from various parent materials and climates. The soil was incubated for 20 days following (i) oxic, (ii) anoxic, and (iii) fluctuating redox conditions. Fungi contributed to 45% of the total GHG under redox fluctuating conditions, including the contribution of bacteria, while the opposite (26%) was valid for oxic treatment. On average, the highest gas emission (62%) was N2O for WRF under redox treatment, followed by anoxic (22%) and oxic (16%) treatments, while CO2 and CH4 emissions followed oxic > redox > anoxic. These data suggest that indigenous microbial WRF communities are well adapted to fluctuating redox milieu with a significant release of GHG emissions in humid temperate forests of the southern cone.

Fine silt and clay content is the main factor defining maximal C and N accumulations in soils: a meta-analysis.

When studying carbon (C) sequestration in soil, it is necessary to recognize the maximal storage potential and the main influencing factors, including the climate, land use, and soil properties. Here, we hypothesized that the silt and clay contents in soils as well as the clay mineralogy are the main factors affecting the maximal C and N storage levels of soils. This hypothesis was evaluated using a database containing the organic C contents of topsoils separated by ultrasonic dispersion to determine the particle size fractions. The slopes of the linear regressions between the C contents in silt and clay to the soil organic C (SOC) and between the N contents in silt and clay to the total N content were independent of the clay mineralogy (2:1, 1:1, calcareous soil, amorphous clays), climate type (tropical, temperate, and Mediterranean), and land use type (cropland, grassland, and forest). This clearly shows that the silt and clay content is the main factor defining an upper SOC level, which allowed us to propose a generalized linear regression (R2 > 0.95) model with a common slope, independent of the land use and climate type, to estimate the soil C sequestration potential. The implications of these findings are as follows: (1) a common slope regression was accurately calculated (0.83 ± 0.02 for C-silt + clay < 63 µm and 0.81 ± 0.02 for C-silt + clay < 20 µm) and (2) there was no asymptotic pattern found to support the existence of an SOC saturation pool.

Contribution of the Fenton reaction and ligninolytic enzymes to soil organic matter mineralisation under anoxic conditions.

Mechanisms of carbon dioxide (CO2) release from soil in the absence of oxygen were studied considering the Fenton process, which encompasses the reaction of H2O2 with Fe(II) yielding a hydroxyl radical (OH), in combination with manganese peroxidase (MnP) and lignin peroxidase (LiP). This study aimed to explain the high rate of soil organic matter (SOM) mineralisation and CO2 release from humid temperate rainforest soils under oxygen-limited conditions. The investigated mechanisms challenge the traditional view that SOM mineralisation in rainforest is slow due to anaerobic (micro)environments under high precipitation and explain intensive CO2 release even under oxygen limitation. We hypothesised that the Fenton reaction (FR) greatly contributes to the CO2 released from SOM mineralised under anaerobic conditions especially in the presence of ligninolytic enzymes. We used a novel technique that combines labelled H218O2 and Fe(II) to induce the FR and measured CO18O, Fe(II) solubilisation, and peroxide consumption in a closed gas circulation system for 6 h. Maximal CO2 amount was released when the FR was induced in combination with LiP addition. The CO2 efflux with LiP was 10-fold that of abiotic FR reactions without enzymes, or in soils amended with MnP. This was consistent with i) the contribution of 18O from peroxide to CO2 release, ii) peroxide consumption, and iii) Fe(II) solubilisation by FR. The amount of consumed peroxide was closely correlated with the CO18O derived from soil without enzyme addition or with LiP addition. Concluding, abiotic Fenton Reaction coupled with oxidative enzymes, such as LiP, are crucial for SOM oxidation under anaerobic conditions, e.g. in temperate rainforest soils.

Iron-reducing bacteria decompose lignin by electron transfer from soil organic matter.

Iron-reducing bacteria (IRB) are crucial for electron transfer in anaerobic soil microsites. The utilization of the energy gathered by this mechanism by decomposers of organic matter is a challenging and fascinating issue. We hypothesized that bacteria reducing Fe(III) (oxyhydr)oxides to soluble Fe(II) obtain electrons from reduced soil organic matter (SOMr) involving lignin oxidation. Iron-reducing bacteria were isolated from topsoils of various climates (humid temperate, cold temperate, subpolar), vegetation types (mostly grasslands and forests), and derived from various parent materials treatments assigned as Granitic, Volcanic-allophanic, Fluvio-glacial, Basaltic-Antarctic and Metamorphic. After the screening of IRB by phospholipid fatty acid (PLFA) analysis and PCR identification (full-length 16S rDNA), the IRB were inoculated to 20 samples (five soils and 4 replicates) and a broad range of parallel processes were traced. Geobacter metallireducens and Geobacter lovleyi were the main Geobacteraceae-strains present in all soils and strongly increased the activity of ligninolytic enzymes: lignin peroxidase and manganese peroxidase. Carbon dioxide (CO2) released from IRB-inoculated soils was 140% higher than that produced by Fenton reactions (induced by H2O2 and Fe(II) addition) but 40% lower than in non-sterile soils. CO2 release was closely correlated with the produced Fe (II) and H2O2 consumption. The highest CO2 was released from Basaltic-Antarctic soils with the highest Fe content and was closely correlated with lignin depolymerization (detection by fluorescence images). All IRB oxidized the lignin contained in the SOM within a wide pH range and in soils from all parent materials. We present a conceptual model showing electron shuttling from SOM containing lignin (as a C and energy source) to IRB to produce energy and promote Fe(III) (oxyhydr)oxides reduction was proposed and discussed.

Synergy effect of peroxidase enzymes and Fenton reactions greatly increase the anaerobic oxidation of soil organic matter.

In temperate rainforest soils of southern Chile (38 °S), there are high rates of soil organic carbon (SOC) mineralization under oxygen (O2) limitation. We study the combined effects of Fenton reactions and the activity of two enzymes manganese peroxidase (MnP) and lignin peroxidase (LiP), which was hypothesised potentiate SOC mineralization under anoxic conditions leading to carbon dioxide (CO2) release. Both mechanisms produce free radicals when competing for SOC oxidation in the absence of microorganisms. We quantify the CO2 release by induced Fenton reactions in combination with MnP and LiP under aerobic and anaerobic conditions (20 °C, 36 h) in temperate rainforest soils. CO2 levels released by Fenton reactions and enzyme activity were eight times higher than those released by Fenton reaction and peroxidase enzymes in individual treatment. Approximately 31% of the CO2 released under aerobic soil incubation was found to be abiotic (sterilized), while 69% was biotic (non-sterilized soils), and respective values of 17% and 83% were recorded under anaerobic conditions. The relative fluorescence intensity clearly shows ·OH radicals production from Fenton reactions. In conclusion, levels of MnP and LiP coupled with Fenton reactions strongly increase SOC mineralization under long periods of O2 limitation in temperate rainforest soils.

Meta-analysis of heavy metal effects on soil enzyme activities.

Enzyme activities (EAs) respond to contamination in several ways depending on the chemical form and content of heavy metals and metalloids (HMs) and their interactions with various soil properties. A systematic and mechanistic understanding of EA responses to HM contamination in soil is necessary for predicting the consequences for nutrient availability and the cycling of carbon (C), nitrogen (N), phosphorus (P) and sulphur (S). In this study, a meta-analysis based on 671 observations found the activities of seven enzymes to decrease in response to soil contamination with Pb, Zn, Cd, Cu and As. HM contamination linearly reduced the activities of all enzymes in the following order: arylsulfatase > dehydrogenase > ß-glucosidase > urease > acid phosphatase > alkaline phosphatase > catalase. The activities of two endoenzymes: arylsulfatase (partly as exoenzyme) and dehydrogenase were reduced by 72% and 64%, respectively. These reductions were two times greater than of exoenzymes: ß-glucosidase, urease, acid phosphatase, alkaline phosphatase and catalase (partly endoenzyme). This reflects the much stronger impact of HMs on living microorganisms and their endoenzymes than on extracellular enzymes stabilized on clay minerals and organic matter. Increasing clay content weakened the negative effects of HM contamination on EAs. All negative effects of HMs on EAs decreased with soil depth because HMs remain mainly in the topsoil. EAs involved in the cycling of C and S were more affected by HMs than the enzymes associated with the cycling of N and P. Consequently, HM contamination may alter the stoichiometry of C, N, P and S released by enzymatic decomposition of organic compounds that consequently affect microbial community structure and activity.

Descripción histológica del aparato reproductor de avestruz hembra (Strutio camelus var. domesticus) / Histological description of the ostrich female reproductive system (Strutio camelus var. domesticus)

El auge de la producción intensiva del avestruz, comenzó en la década de los noventa impulsada por la calidad de su carne y potencialidad de sus subproductos. La raza empleada para producción por la calidad nutricional y sabor de su carne es el híbrido llamado African black (Struthio camelus var. domesticus). En cuanto a la reproducción, el avestruz hembra alcanza su madurez sexual a partir de los 2,5 años. Es importante considerar el aparato genital en aves de producción, ya que una alteración en él, puede generar deficiencias en la fertilidad que se traducen en un menor número de crías. El estudio histológico del aparato reproductor de la hembra será una herramienta más que permitirá resolver problemas reproductivos. Para este análisis se obtuvo muestras de los diferentes segmentos del aparato reproductor de 6 avestruces hembras en edad reproductiva y se procesaron de acuerdo a las técnicas histológicas de rutina. Los cortes fueron observados, fotografiados y analizados bajo microscopio de luz. Obtenidas las fotografías, se analizó comparativamente su morfología con la descrita en la gallina (Gallus gallus). El aparato reproductor de la hembra tiene la particularidad de tener desarrollado solo el ovario y oviducto izquierdo. El ovario es de gran tamaño y en forma de racimo, el cual varía según la estacionalidad. Presenta folículos primordiales, previtelogénicos, vitelogénicos y atrésicos. Los folículos vitelogénicos presentan células de la granulosa y de la teca interna y externa. El oviducto presenta de cefálico a caudal los siguientes segmentos: infundíbulo, magnum, istmo, útero y vagina, que desemboca en la cloaca a nivel del urodeo. En ellos hay pliegues de variada longitud, grosor y número que comprometen la mucosa y submucosa, con glándulas de secreción mucosa y serosa a excepción de la vagina. El análisis histológico comparativo, permitió establecer que la morfología del aparato reproductor de la hembra es semejante a la observada en la gallina con ciertas diferencias microscópicas (Gallus gallus).

In the 1990's, ostrich production reached a peak in our country, boosted by the special characteristics of its meat and the potential of the derivatives. The breed raised is a hybrid called African Black (Struthio camelus var. domesticus) which has a high quality meat in terms of nutritional factors and flavor. With regard to reproduction, the female ostrich reaches maturity at the age of 2.5 years. Genital organs are very important in fowl's production, because they can generate fertility deficiencies that, in turn can diminish brood number. Histological analysis allows a better understanding of the basic structure of the female's genital organs and is a helpful tool to resolve breeding problems. For this analysis samples were obtained from the different segments of the reproductive system of 6 female ostrich in reproductive age. These samples were processed using standard histological technique. Sections were observed, photographed and analyzed under the light-microscope. Photographs were compared with hen's samples. The ostrich female's reproductive system has the particularity of having just the left ovary and oviduct developed. The ovary has a big size and a cluster shape which varies from season to season. It presents paramount, previtellogenic, vitellogenic and atresic follicles. The vitellogenic follicles have granulosa cells and inner and external theca. The oviduct presents cephalocaudally: infundibulum, magnum, isthmus, uterus and vagina, flowing into the urodeum. It shows long pleats of different length and number, with drusen of mucose and serose secretion, except in the vagina. The comparative histological analysis allowed us to establish that the basic structure of the female reproductive system is similar to that of the hen (Gallus gallus).

Animal model of Mycoplasma fermentans respiratory infection.

BACKGROUND: Mycoplasma fermentans has been associated with respiratory, genitourinary tract infections and rheumatoid diseases but its role as pathogen is controversial. The purpose of this study was to probe that Mycoplasma fermentans is able to produce respiratory tract infection and migrate to several organs on an experimental infection model in hamsters. One hundred and twenty six hamsters were divided in six groups (A-F) of 21 hamsters each. Animals of groups A, B, C were intratracheally injected with one of the mycoplasma strains: Mycoplasma fermentans P 140 (wild strain), Mycoplasma fermentans PG 18 (type strain) or Mycoplasma pneumoniae Eaton strain. Groups D, E, F were the negative, media, and sham controls. Fragments of trachea, lungs, kidney, heart, brain and spleen were cultured and used for the histopathological study. U frequency test was used to compare recovery of mycoplasmas from organs. RESULTS: Mycoplasmas were detected by culture and PCR. The three mycoplasma strains induced an interstitial pneumonia; they also migrated to several organs and persisted there for at least 50 days. Mycoplasma fermentans P 140 induced a more severe damage in lungs than Mycoplasma fermentans PG 18. Mycoplasma pneumoniae produced severe damage in lungs and renal damage. CONCLUSIONS: Mycoplasma fermentans induced a respiratory tract infection and persisted in different organs for several weeks in hamsters. This finding may help to explain the ability of Mycoplasma fermentans to induce pneumonia and chronic infectious diseases in humans.