Controlled comparisons between soil and hydroponic systems reveal increased water use efficiency and higher lycopene and ß-carotene contents in hydroponically grown tomatoes.

There are many different types of systems used to grow food that are distinguished by ideology or the technology used. It is often difficult to directly compare yield and quality in different growth systems due to the complicated interactions between genotype, physiology and environment. Many published comparisons do not identify and acknowledge confounding factors. However, there is urgency to undertake controlled comparisons to identify the most efficient and effective food production systems, because the world faces considerable challenges to food supply with population rise, ongoing environmental degradation and the threat of climatic change. Here we compared soil with two hydroponic growth systems, drip irrigation and deep-water culture (DWC). It is often claimed that such systems differ in water use, yield and crop quality; however, such comparisons are often confounded by assessing plant and system parameters in different growth environments or where factors that are difficult to standardise between systems, such as nutrient status, are not controlled. We grew tomato (Solanum lycopersicum L.) in the three growth systems in two replicated experiments, in either a polytunnel or glasshouse. We controlled and monitored water use and nutrient levels across all systems as different fertilizer applications can influence the nutritional values of produce. Plants in the two hydroponic systems transpired less water and were more water-efficient with a lower product water use than plants grown in soil. Fruit yield was similar and total soluble solids and sugar levels were not significantly different between the three growing systems. However, levels of lycopene and ß-carotene were either similar or significantly higher in DWC compared to growth systems using soil or drip irrigation. Our results identify hydroponic systems as more water use efficient with DWC also capable of producing higher quality produce.

Variation in Soil Fungal Composition Associated with the Invasion of Stellera chamaejasme L. in Qinghai-Tibet Plateau Grassland.

Stellera chamaejasme L. is the most problematic weed in China's grasslands. Its root exudates affect co-occurring plants and thus may also affect soil fungi. Soils (0-20 cm depth) on two adjacent sites, one invaded the other uninvaded, were compared for a range of physiochemical parameters and by DNA sequencing of fungal communities. At the invaded site, relationships between S. chamaejasme abundance, soil physiochemical factors, and fungal communities were further investigated to determine whether these relationships corroborated conclusions on the basis of site differences that could be translated into functional variation. Results showed that the invaded soils had lower N, P, organic matter, fungal alpha diversity, and relative abundance of arbuscular mycorrhizal fungi (AMF), but greater abundance of pathogenic fungi. Organic matter and P were the edaphic factors most strongly linked to site differences in total fungal communities. Within the invaded site, organic matter rather than S. chamaejasme cover was closely linked to total fungal composition. However, on this site, a number of fungal species that had various ecological functions and that differentiated the two sites were related to S. chamaejasme cover. This study indicates that lower fertility soils may be more susceptible to invasion by S. chamaejasme. Although the influence of S. chamaejasme on total fungal community composition was limited, there was evidence of effects on particular fungal species. Further research is needed to determine whether these effects influence S. chamaejasme invasiveness.

Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications.

Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.

Genome Sequence Analysis of Two Pseudomonas putida Strains to Identify a 17-Hydroxylase Putatively Involved in Sparteine Degradation.

Two strains of Pseudomonas putida, Psp-LUP and Psp-SPAR, capable of growth on the quinolizidine alkaloids, lupanine and sparteine respectively, were studied here. We report the isolation of Psp-SPAR and the complete genome sequencing of both bacteria. Both were confirmed to belong to P. putida, Psp-LUP close to the type isolate of the species (NBRC14164T) and Psp-SPAR close to strains KT2440 and F1. Psp-SPAR did not grow on lupanine but did contain a gene encoding a putative quinolizidine-17-hydroxylase peptide which exhibited high similarity (76%identity) to the lupanine-17-hydroxylase characterised from Psp-LUP.

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap.

Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps.

Copper deficiency in potato dextrose agar causes reduced pigmentation in cultures of various fungi.

Potato dextrose agar (PDA) is one of the most commonly used media for the isolation and cultivation of fungi, with morphological features and pigmentation in culture often being important for identification of cultures. Cultivation of various fungi on different brands and batches of powdered (commercial) potato dextrose media revealed deficient pigmentation in five of 10 media tested. Reduced pigmentation on these media was correlated with low levels of copper and colony colour was restored by the addition of copper. Deficient pigmentation was most pronounced when copper levels in the medium were below 50 ng mL(-1) (50 p.p.b.; 0.8 microM). Differences in pigmentation and laccase activity of spore and mycelial preparations were quantified for representative species belonging to the genera Aspergillus, Fusarium, Trichoderma, Cladosporium and Penicillium grown on PDA containing different amounts of copper. A strong positive correlation between laccase activity and copper levels was observed. Differences were also found between batches of raw potatoes, with organically cultivated tubers having higher copper levels than those grown by conventional methods, possibly because of the use of copper-based fungicides in the former case. Routine addition of 1000 ng mL(-1) copper (or standard trace element solutions) to PDA and other undefined media is advised to avoid atypical culture pigmentation and possibly other consequences of reduced activity of copper-requiring enzymes.