Linking nitrogen cycling transformations to microbial diversity in freshwater ecosystems

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Effect of Heavy Metals on the Growth of Bacteria Isolated from Sewage Sludge Compost Tea

Abstract The amount of urban sewage sludge is increasing daily. For this reason, it is necessary to have an environmentally friendly use for this residue. Land applications in olive grove soil, poor quality soil, as a compost or a compost tea could be considered as one of the best options, because it has a high content of organic matter. However, the presence of heavy metals in some sewage sludge could be an environmental problem. In this sense, the aim of this work is to check the tolerance of the culturable microbiota present in sewage sludge compost tea to four heavy metals, Cu, Cd, Pb and Zn. Among microbiota isolated, eight strains showed high resistance to Pb, Zn, Cu and Cd, and one microbe (Rhodococcus sp.) showed a special tolerance to every heavy metal. The strains were divided into six genrera: Rhodococcus, Virgibacillus, Leifsoni, Achromobacter, Cupriavidus and Oceanobacillus sp. Finally, Rhodococcus sp. strain 3 was able to remove different amounts of heavy metals from the culture media with intracellular and surface accumulation of Cu, Zn, Pb and Cd. The application of this bacterial strain in bioremediation processes is discussed

Elucidating three-way interactions between soil, pasture and animals that regulate nitrous oxide emissions from temperate grazing systems

Pasture-based livestock farming contributes considerably to global emissions of nitrous oxide (N2O), a powerful greenhouse gas approximately 265 times more potent than carbon dioxide. Traditionally, the estimation of N2O emissions from grasslands is carried out by means of plot-scale experiments, where externally sourced animal excreta are applied to soils to simulate grazing conditions. This approach, however, fails to account for the impact of different sward types on the composition of excreta and thus the functionality of soil microbiomes, creating unrealistic situations that are seldom observed under commercial agriculture. Using three farming systems employing contrasting pasture management strategies at the North Wyke Farm Platform, an instrumented ruminant grazing trial in Devon, UK, this study measured N2O emissions from soils treated with cattle urine and dung collected within each system as well as standard synthetic urine shared across all systems, and compared them against two forms of controls with and without inorganic nitrogen fertiliser applications. Soil microbial activity was regularly monitored through gene abundance to evaluate interactions between sward types, soil amendments, soil microbiomes and, ultimately, N2O production. Across all systems, N2O emissions attributable to cattle urine and standard synthetic urine were found to be inconsistent with one another due to discrepancy in nitrogen content. Despite previous findings that grasses with elevated levels of water-soluble carbohydrates tend to generate lower levels of N2O, the soil under high sugar grass monoculture in this study recorded higher emissions when receiving excreta from cattle fed the same grass. Combined together, our results demonstrate the importance of evaluating environmental impacts of agriculture at a system scale, so that the feedback mechanisms linking soil, pasture, animals and microbiomes are appropriately considered

A simultaneous search for High-z LAEs and LBGs in the SHARDS survey

We have undertaken a comprehensive search for both Lyman Alpha Emitters (LAEs) and Lyman Break Galaxies (LBGs) in the SHARDS Survey of the GOODS-N field. SHARDS is a deep imaging survey, made with the 10.4 m Gran Telescopio Canarias (GTC), employing 25 medium band filters in the range from 500 to 941 nm. This is the first time that both LAEs and LBGs are surveyed simultaneously in a systematic way in a large field. We draw a sample of 1558 sources; 528 of them are LAEs. Most of the sources (1434) show rest-frame UV continua. A minority of them (124) are pure LAEs with virtually no continuum detected in SHARDS. We study these sources from z ∼ 3.35 up to z ∼ 6.8, well into the epoch of reionization. Note that surveys done with just one or two narrow band filters lack the possibility to spot the rest-frame UV continuum present in most of our LAEs. We derive redshifts, Star Formation Rates (SFRs), Lyα Equivalent Widths (EWs) and Luminosity Functions (LFs). Grouping within our sample is also studied, finding 92 pairs or groups of galaxies at the same redshift separated by less than 60 comoving kpc. In addition, we relate 87 and 55 UV-selected objects with two known overdensities at z = 4.05 and z = 5.198, respectively. Finally, we show that surveys made with broad band filters are prone to introduce many unwanted sources (∼20% interlopers), which means that previous studies may be overestimating the calculated LFs, specially at the faint end

Agronomical parameters of host and non-host legumes inoculated with Melilotus indicus-isolated rhizobial strains in desert unreclaimed soil

In a search for identification of rhizobial strains with superior N-fixation efficiency and improved plant agronomic characteristics upon inoculation, four strains, 4.21, 9.17, 11.2 and 14.1, isolated from root nodules of wild-grown Melilotus indicus have been used to inoculate field-grown common bean, pea, cowpea and fenugreek plants. Uninoculated plants and those inoculated with host-specific commercial inoculants were used as a control. The root length, shoot height, shoot dry weight and root dry weight and the grain yield of the plants were determined after harvest. The content of N, organic C and carbohydrates content of the grain were also recorded. The inoculation with the strains 4.21 and 14.1 increased the grain yield of the fenugreek compared both with the uninoculated plants and those inoculated with the commercial strain ARC-1. The grain yield of the common bean treated with the strains 9.17 and 14.1 was also higher than that of the uninoculated and the commercial strains ARC-301. In contrast, none of the strains increased the grain yield of the pea and cowpea plants compared to the commercial strains ARC-201 and ARC-169, respectively. Significant increases of some agronomical parameters were observed in some plant–bacterium couples, albeit nodulation was not observed. It is possible that the positive effects of rhizobial inoculation on the agronomical parameters of the non-nodule forming legumes could be due to plant growth promotion characteristic of the strains used for inoculation. Analysis of the phylogeny of the almost complete 16S rRNA sequence of the rhizobial inoculants revealed that the strains 4.21 and 9.17 clustered together with R. skierniewicense and R. rosettiformans, respectively, and that the strains 11.2 and 14.1 grouped with E. meliloti. All the four strains produced IAA, and showed biocontrol activity against Rhizotocnia solani, Fusarium oxysporum, Pythium ultimum, Alternaria alternata and Sclerotonia rolsfi, albeit to a different extent.Financial support was also obtained from the ERDF-cofinanced project AGL2017–85676R from Ministerio de Economía, Industria y Competitividad (Spain)

Phylogenetic diversity of Bradyrhizobium strains isolated from root nodules of Lupinus angustifolius grown wild in the North East of Algeria

From a total of 80 bacterial strains isolated from root nodules of Lupinus angustifolius grown wild in the North-Eastern Algerian region of El Tarf, 64 plant host-nodulating strains clustered into 17 random amplified polymorphic DNA (RAPD) fingerprinting groups. The nearly complete 16S rRNA gene sequence from the representative strain of each group revealed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but their affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis, showed that 12 strains belong to B. lupini, other 2 strains affiliated with B. diazoefficiens and that 1 strain was closely related to B. japonicum. The remaining two strains showed similarity values ≤95% with B. cytisi and could represent new lineages within the genus Bradyrhizobium. Sequencing of the symbiotic nodC gene from 4 selected bradyrhizobial strains showed they were all similar to those of the species included in symbiovar genistearum.This study was supported by the ERDF-cofinanced grants PEAGR2012-1968 from Consejería de Economía, Innovación y Ciencia (Junta de Andalucía, Spain), AGL2015-64582-C3-3-R from MINECO. ACH is recipient of a grant of MECD (FPU 2014/01633).Peer Reviewe

Physicochemical variables better explain changes in microbial community structure and abundance under alternate wetting and drying events

Soil microbial communities play an important role in nutrient cycling; however, their response under repeated long-term fertilization has attracted little attention and needs further appraisal. A 14-day incubation study compared the relative abundance, diversity, and composition of bacterial and fungal microbial communities in soils treated with long-term applications of chemical fertilizer (CF), pig manure plus chemical fertilizer (PMCF), and rice straw plus chemical fertilizer (SRCF) in a paddy field. A high-throughput sequencing approach was applied to assess the diversity and composition of microbial community. Results revealed the Shannon index of the bacterial community decreased with fertilizer addition but increased in case of fungal community. The abundance of the Actinobacteria was higher in the PMCF, while Proteobacteria were higher in the CF and SRCF treatments than those in the unamended control under alternate wetting and drying (AWD) and permanent flooding (PF). In addition, chemical fertilizer history increased the abundance of Firmicutes under AWD. Initially, Nitrospira were found higher in the unamended control than in the amended treatments, but an increase was observed with time in fertilized treatments. Among all genera, Proteobacteria were the most abundant bacterial genus. The main properties that markedly affected the bacterial communities were SOC (R² = 0.4037, p < 0.02), available P (R² = 0.3273, p < 0.05), and NO₃− (R² = 0.3096, p < 0.08). Soil physicochemical factors and biogenic factors explained a variation of 46.27% and 29.35%, respectively. At the same time, 4.59% was the combined effect of physicochemical and biogenic factors. Our results suggested that the physicochemical properties had a more significant impact on bacterial activities than water regime by increasing N and organic matter concentrations in the soils

Phylogenetic diversity of Bradyrhizobium strains isolated from root nodules of Lupinus angustifolius grown wild in the North East of Algeria

From a total of 80 bacterial strains isolated from root nodules of Lupinus angustifolius grown wild in the North-Eastern Algerian region of El Tarf, 64 plant host-nodulating strains clustered into 17 random amplified polymorphic DNA (RAPD) fingerprinting groups. The nearly complete 16S rRNA gene sequence from the representative strain of each group revealed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but their affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis, showed that 12 strains belong to B. lupini, other 2 strains affiliated with B. diazoefficiens and that 1 strain was closely related to B. japonicum. The remaining two strains showed similarity values ≤95% with B. cytisi and could represent new lineages within the genus Bradyrhizobium. Sequencing of the symbiotic nodC gene from 4 selected bradyrhizobial strains showed they were all similar to those of the species included in symbiovar genistearum.This study was supported by the ERDF-cofinanced grants PEAGR2012-1968 from Consejería de Economía, Innovación y Ciencia (Junta de Andalucía, Spain), AGL2015-64582-C3-3-R from MINECO. ACH is recipient of a grant of MECD (FPU 2014/01633).Peer Reviewe