Wildfires are a recurrent disturbance in Mediterranean forests, triggered by high fuel load, high environmental temperature and low humidity. Although, human intervention is behind the initiation of ...most fire episodes, the situation is likely to worsen in the future due to the effects of climate change in the Mediterranean “hot-spot”. Here we study chemical, physical and microbial characteristics of burnt soils from two well differentiated sites at Sierra de Cazorla, Segura and Las Villas Natural Park, Andalusia, (Spain) affected and unaffected by a wildfire, and followed their evolution for three years. The soils affected by a severe surface burn showed a significant increase in organic matter after 3years from the fire. Viable bacteria and fungi also increased, especially 2–3years post-burning. Substrate induced respiration (SIR) also increased significantly in burnt soil from site 1 (rendzina on carbonate) while a significant decrease was observed in the burnt soils sampled from site 2 (calcic luvisols) in samples taken one month after the wildfire. A recovery in both SIR and organic matter was observed after 2 and 3years. Of seven soil enzymes studied, only phosphatase activity was significantly higher in most burnt soils over the three years. Analysis of bacterial community diversity using clone libraries showed a recovery in the number of phyla in burnt soils after 2 and 3years in both sites, with an increase in Proteobacteria and Firmicutes and a decrease in Acidobacteria phyla. For Bacteroidetes, the percentages were lower in most burnt samples. This study reveals that if wildfire increases the organic matter availability, then the microbial community responds with increased activity and biomass production. Although fire exerts an initial impact on the soil bacterial community, its structure and functional profile soon recovers (after 2–3years) contributing to soil recovery.
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•Physico-chemical and microbial characteristics of fire affected soils are studied.•Fire increased soil N, soil OM and phosphatase activity.•Proteobacteria and Firmicutes phyla increased in burnt soil.•Acidobacteria and Bacteroidetes phyla decreased in burnt soil.•Microbes respond to soil OM with higher diversity, activity and biomass production.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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•AMF occurrence, diversity and community composition were investigated in apple roots.•High levels of mycorrhizal colonization were found in 21 South Tyrol apple orchards.•Two ...molecular methods, PCR cloning and sequencing and PCR-DGGE, were used.•For the first time native AMF in apple roots were identified at the species level.•Geographical area, management and altitude affected AMF diversity in apple roots.
Arbuscular mycorrhizal fungi (AMF) are beneficial microrganisms which establish mutualistic symbioses with the roots of most food crops, improving plant performance, nutrient uptake and tolerance to biotic and abiotic stresses. A better understanding of the factors affecting AMF occurrence and diversity is fundamental to implement sustainable agricultural managements effectively profiting from beneficial plant symbionts. Here, we investigated AMF occurrence, diversity and community composition in the roots of apple trees from 21 orchards in South Tyrol, as affected by location, management (organic vs integrated) and altitude, by PCR cloning and sequencing and PCR-DGGE of partial 18S rRNA gene. The screening of 448 clones from 21 clone libraries allowed the identification of 6 native AMF at the species level: Glomus indicum, Sclerocystis sinuosa, Funneliformis mosseae, Rhizoglomus irregulare, Septoglomus constrictus and Claroideoglomus lamellosum. The most abundant genera were represented by Glomus (29.7% of the sequences), Paraglomus (19.4%), Claroideoglomus (17.2%), Sclerocystis (16.1%) and Rhizoglomus (12.3%). Septoglomus, Diversispora and Funneliformis sequences corresponded to less than 4% of total sequences. Although the degree of root colonization was unaffected by treatments, ANOSIM analysis of PCR-DGGE clusters revealed significant differences in apple root AMF diversity between sites and agricultural managements. Species richness was significantly higher in organically managed orchards than in integrated ones. Our findings provide insights into important factors affecting native AMF communities of apple trees, which could be exploited in sustainable fruit production systems, where beneficial soil biota boost biogeochemical cycles, energy fluxes and crop productivity.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Abstract
Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal ...communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season. This pattern was confirmed by clone libraries of winter and summer samples: we obtained 720 16S rRNA gene sequences that represented 44 operational taxonomic units (OTUs) within the phylum Planctomycetes. Most of the OTUs belonged to Blastopirellula, followed by Rhodopirellula, Planctomyces, the Pir4 lineage and the uncultured class OM190 (this last one nearly 30% of the OTUs). Ulva sp. and C. crispus had more diverse planctomycetal communities than F. spiralis. Analysis of beta diversity showed that the planctomycetal microbiome was host specific. We hypothesize that the specific association of Planctomycetes and their macroalgal hosts is likely determined by nutritional molecules provided by the algae and the set of sulfatases inherent to each Planctomycetes species.
The epiphytic planctomycetal communities on three macroalgae are significantly host specific which may be determined by nutritional molecules provided by the alga.
We analysed and characterized the cyanobacteria in microbialites of Alchichica crater lake over a depth gradient, from 3 to 30 m. A polyphasic approach was followed using morphometry, optical and ...epifluorescence microscopy, and molecular methods. Regions V3-V4 of the 16S rRNA conserved for cyanobacteria were amplified and used for clone library construction. Independently, a NGS library was constructed using the V4 region of the 16S rRNA. To complement the analysis, eight monocultures of cyanobacteria were isolated from microbialites, which were also characterized by microscopy and 16S rRNA sequencing. In total, we described 18 genera of cyanobacteria isolated from microbialites of Alchichica crater lake. The distribution pattern suggests that on the surface there were mostly Nostocales and filamentous Synechococcales, while at depth we found single-celled Synechococcales. Pleurocapsales and Chroococcales were found at all depths, increasing in abundance at 20 and 30 m.
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BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Aims
The aim of this study was the baseline description of oil‐degrading sediment bacteria along a depth transect in the Faroe‐Shetland Channel (FSC) and the identification of biomarker taxa for the ...detection of oil contamination in FSC sediments.
Methods and Results
Oil‐degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture‐dependent and culture‐independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well‐known oil‐degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold‐water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m.
Conclusions
The genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep‐sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general.
Significance and Impact of the Study
Oil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
•Adding manganese ions would cause disintegration of aerobic granules.•Contents of c-di-GMP were reduced in the presence of manganese ions.•Contents of extracellular polysaccharides and proteins ...decreased with manganese ions.•Polysaccharide producers were lost with added manganese ions.•c-di-GMP is key chemical factor epistatic to quotum sensing to granular stability.
Loss of structural stability of aerobic granular process is the challenge for its field applications to treat wastewaters. The second messenger, cyclic diguanylate (c-di-GMP), is widely used by bacteria to regulate the synthesis of exopolysaccharide. This study for the first time confirmed the correlation between concentration of intracellular c-di-GMP and the granular stability under sequencing batch reactor (MBR) mode. In the presence of manganese ions (Mn2+), the concentrations of intracellular c-di-GMP and of extracellular polysaccharides and proteins in granules were declined. Clone library study revealed that the polysaccharide producers. Acinetobacter sp., Thauera sp., Bdellovibrio sp. and Paracoccus sp. were lost after Mn2+ addition. The findings reported herein confirmed that the c-di-GMP is a key chemical factor epistatic to quorum sensing to determine granular stability. Stimulation of synthesis of intracellular c-di-GMP presents a potential way to enhance long-term stability of aerobic granules.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
A set of chemical, physical and microbial characteristics of different burnt soils from Sierra de Aznalcóllar (Sevilla, Spain) affected by one or two sequential fires, were analysed and compared with ...those of their respective control soils. A decrease in total organic carbon was observed in burnt soils, which could be attributed to the impact of the fires on vegetation cover. Biomass (estimated as viable and culturable microorganisms), substrate-induced respiration (SIR) and activity of different soil enzymes involved in carbon, nitrogen and phosphorus cycles were determined to assess the effect of fire on total microbial populations and on soil activity. An increase in both bacterial and fungal biomass as well as respiratory activity was detected in most burnt soils. In terms of enzyme activity, no common pattern of behaviour was observed, except for the alkaline phosphatase activity, which showed increased levels in all the burnt soils. The effect of fire on microbial diversity was estimated for Bacteria and Archaea domains from DNA band patterns obtained in denaturing gradient gel electrophoresis (DGGE), as well as using 16S rRNA cloned sequences for Bacteria. Shannon index values obtained from the DGGE profiles showed higher diversity for both Bacteria and Archaea domains in burnt soils compared with the control ones. Variations in the number of different phyla present in burnt and control soils were inferred from the analysis of the 16S rRNA cloned sequences. However, in all areas the most important groups identified belonged to the Proteobacteria, Acidobacteria and Actinobacteria phyla. No differences between microbial communities present in burnt soils at the genus level were detected.
•Physico-chemical and microbial characteristics of fire affected soils are studied.•Microbial biomass and diversity were higher in burned than in control soils.•Impact of fire on soil microbiota was not directly dependent upon fire recurrence.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
•Higher diversity of bacteria was found in high concentration swine wastewater.•Bacterial diversity was strongly positive correlation with DO.•Bacterial community distribution was strongly positive ...correlations with N and P.•Proteobacteria played an indispensable roles in M. elatinoides purification system.•Bacterial community dynamics was responsive to swine wastewater treating process.
Constructed wetlands are important ecological tools for treating municipal, industrial, and agricultural wastewater. Terminal restriction fragment length polymorphisms and clone libraries were employed to determine the variation in bacterial community diversity and structure from a Myriophyllum elatinoides purification system used to treat different concentrations of swine wastewater. Experiments included tap water (control), a low concentration of swine wastewater (S1, 200ppm NH4+), and a high concentration of swine wastewater (S2, 400ppm NH4+) in small tanks. The total nitrogen (TN) and total phosphorus (TP) removal efficiency were equal to or greater than 93.9% and 93.1%, respectively, in 28d. Higher diversity of bacteria was found in S2 on day 7 and day 14. In total, 221 genera representing 17 phyla were detected. Acidobacteria and Proteobacteria dominated at the phylum level in sediments, with relative abundance ranging from 33.3% to 50% and 26.2 to 42.9%, respectively. Proteobacteria was primarily represented by Betaproteobacteria and Deltaproteobacteria at the class level on days 7, 14, and 28, and Nitrospira was detected on day 7. Verrucomicrobia was positively related to NH4+ (Pearson’s correlation, P<0.05), Bacteroidetes was negatively related to NH4+ (P<0.05). Redundancy analysis revealed that the bacterial community distribution was strongly positively correlated with TN, ammonia, TP, and phosphate in S1 and S2, these environmental parameters had a much stronger effect on S2 than S1. However, the bacterial diversity was strongly positively correlated with dissolved oxygen (P<0.01). Certain bacteria were implicated in nitrogen and phosphorus removal in the M. elatinoides purification system, and the bacterial community dynamics changed as the environmental factors were altered during purification, therefore, wastewater parameters could predict the microbial community structure. Our results reveal microbial N and P removal process, which are important for M. elatinoides purification system studies in the field.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
This study aimed at determining bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and their surrounding brackish waters and sediment. Freshly caught shrimp, water and ...sediment samples were collected in Lakes Nokoue and Aheme in Benin (West Africa) during two periods with different water salinity and temperature. We used complementary culture-dependent and culture-independent methods for microbiota analysis. During both sampling periods, total mesophilic aerobic counts in shrimp samples ranged between 4.4 and 5.9logCFU/g and were significantly higher than in water or sediment samples. In contrast, bacterial diversity was higher in sediment or water than in shrimps. The dominant phyla were Firmicutes and Proteobacteria in shrimps, Firmicutes, Proteobacteria, and Actinobacteria in water, and Proteobacteria and Chloroflexi in sediment. At species level, distinct bacterial communities were associated with sediment, water and shrimps sampled at the same site the same day. The study suggests that the bacterial community of tropical brackish water shrimps cannot be predicted from the microbiota of their aquatic environment. Thus, monitoring of microbiological quality of aquatic environments might not reflect shrimp microbiological quality.
•Bacterial concentration and diversity were determined in shrimps, water and sediment.•Bacterial concentration was higher in shrimps than in water or sediment.•Bacterial diversity was higher in sediment or water than in shrimps.•Distinct bacterial communities were associated with shrimps, water and sediment.•Bacterial community of shrimps cannot be predicted from that of their environment.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Phylum- and class-specific PCR primers were tested for the production of clone libraries and for denaturing gradient gel electrophoresis (DGGE) analysis of complex bacterial communities. Primers were ...designed to specifically amplify 16S rRNA gene fragments of the phyla Bacteroidetes, Planctomycetes and Firmicutes, of three classes of the phylum Proteobacteria, the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, and of the Cyanobacteria (including chloroplast 16S rRNA genes). The specificity of the seven primer pairs was tested by producing clone libraries from environmental DNA samples from mesotrophic (Norwegian coastal) and oligotrophic (Northern Atlantic Gyre) environments. Five of the seven primer pairs specifically amplified target 16S rRNA gene sequences. Exceptions were the Betaproteobacteria- and Firmicutes-specific primers, which were relatively successful with coastal water mesocosm samples but less so with the Northern Atlantic Gyre sample. Phylogenetic analysis of sequences from the Gammaproteobacteria clone library revealed that the coastal sample yielded a number of clones that clustered within clades that belong to the oligotrophic marine Gammaproteobacteria (OMG) group, indicating that this group is not confined exclusively to the oligotrophic environment. Comparison of the bacterial diversity of the environmental DNA sample from the coastal and the open ocean using a two- or three-step nested PCR-DGGE process revealed significant differences in the bacterial communities. The application of the group-specific primers provides a higher resolution genetic fingerprinting approach than existing DGGE primer sets.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, SBNM, UL, UM, UPUK
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