Bacterial communities and predicted nitrogen metabolism of heterotrophic‐ and probiotic‐based biofilms used for super‐intensive indoor shrimp culture

Biofilm‐based aquaculture systems constitute a promising alternative for intensive shrimp rearing. Microorganisms forming biofilms can recycle the nitrogen compounds the production units improving the water quality while using zero or limited water exchange. This study aimed to compare the taxonomic profiles and the predicted functions related to the transformation of nitrogenous compounds between a heterotrophic‐ (HtB) and a probiotic biofilm (PrB), and the effect of these on the water quality and the productive response of cultured shrimp. Libraries of the 16S‐rRNA gene (V3‐V4 region) were prepared and sequenced to be used as a taxonomic biomarker. Analysis of metagenomic datasets revelated that genera Halomonas, Planctomycetes and Rhodopirellula were the most abundant genera in HtB; meanwhile, Bacillus, Halobacillus and Flavobacterium dominated in PrB. Regarding nitrogen metabolism, the proportion of genes encoding enzymes catalyzing the six pathways shaping the nitrogen metabolism showed differences between biofilms, which could also explain the difference in water quality between treatments. Concerning the productive response of shrimp, no significant differences were detected except for survival, which was higher in PrB. Finally, the results suggest that biofilms harbour functions for nitrogen metabolism, including dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, nitrification, nitrogen fixation and anammox; however, the balance of these functional capabilities seems to be relevant to maintain water quality.     

Changes in digestive enzyme activities during the early ontogeny of the South American cichlid (Cichlasoma dimerus)

Fish Physiology and Biochemistry - Cichlasoma dimerus is a neotropical cichlid that has been used as a biological model for neuroendocrinology studies. However, its culture is problematic in terms...     

A case of yellow fever in a brown howler (Alouatta fusca) in Southern Brazil.

Many brown howlers (Alouatta fusca) have died in a 3-month period in a subtropical forest in Southern Brazil. One was examined after a systemic illness. According to clinical signs, and necropsy and histopathology findings, yellow fever virus (YFV) infection was suspected. Tissue sections from liver, kidney, and lymphoid organs were screened by immunohistochemistry for YFV antigens. Cells within those tissues stained positively with a polyclonal antibody against YFV antigens (1:1,600 dilution), and yellow fever was diagnosed for the first time in the brown howler in the area.     

Apatite Control of Phosphorus Release to Runoff from Soils of Phosphate Mine Reclamation Areas

This study was initiated to explore the effects of ozone (O₃) exposure on potted wheat roots and soil microbial community function. Three treatments were performed: (1) Air with daily averaged O₃ concentration of 4–10 ppb (control situation, CK), (2) Air plus 8 h averaged O₃ concentration of 76.1 ppb (O₃-1), and (3) Air plus 8 h averaged O₃ concentration of 118.8 ppb (O₃-2). In treatments with elevated O₃ concentration (O₃-1 and O₃-2), the root and shoot biomass were reduced by 25% and 18%, respectively, compared to the control treatment (CK). On the other hand, root activity was significantly reduced by 58% and 90.8% in the O₃-1 and O₃-2 treatments, respectively, compared to CK. The soil microbial biomass was significantly reduced only in the highest O₃ concentration (O₃-2 treatment) in the rhizosphere soil. Soil microbial community composition was assessed under O₃ stress based on the changes in the sole carbon source utilization profiles of soil microbial communities using the Biolog? system. Principal component analysis showed that there was significant discrimination in the sole-carbon source utilization pattern of soil microbial communities among the O₃ treatments in rhizosphere soil; however, there was none in the bulk soil. In rhizosphere soil, the functional richness of the soil microbial community was reduced by 27% and 38% in O₃-1 and O₃-2 treatments, respectively, compared to CK. O₃-2 treatment remarkably decreased the Shannon diversity index of soil microbial community function in rhizosphere soil, but the O₃-1 treatment did not. In the dominant microorganisms using carbon sources of carbohydrates and amino acids groups were significantly reduced by an elevated O₃ concentration in the rhizosphere soil. Our study shows that the elevated ozone levels may alter microbial community function in rhizosphere soil but not in the bulk soil. Hence, this suggests that O₃ effects on soil microbes are caused by O₃ detriments on the plant, but not by the O₃ direct effects on the soil microbes.     

Genetic and bioclimatic variation in <Emphasis Type="Italic">Solanum pimpinellifolium</Emphasis>

Solanum pimpinellifolium, due to its close relationship to S. lycopersicum, has been a genetic source for many commercially important tomato traits. It is a wild species found in the coastal areas of Peru and Ecuador. In this study, the genetic variation of S. pimpinellifolium was studied using the diversity found in 10 microsatellites in 248 plants spread throughout its entire distribution area, including Ecuador, which has been underrepresented in previous studies. Peruvian and Ecuadorian accessions are genetically quite differentiated. A possible cause of these differences could be the non-uniform nature of the coastal Ecuadorian and Peruvian climates, seeing as an important correlation between genetic differentiation and climate has been found. In addition, Ecuadorian and south Peruvian accessions have a lower genetic diversity and a higher homozygosity due to their higher autogamy, lower population size, and possible colonization bottlenecks. The Galápagos Islands population is an extreme case, with no diversity, likely caused by a recent colonization from the northern continental Ecuadorian region where genetically identical plants have been found. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Elena Zuriaga and José M. Blanca contributed equally to this work.     

Development of molecular markers linked to the <Emphasis Type="Italic">Fom-1</Emphasis> locus for resistance to Fusarium race 2 in melon

Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (F.o.m), is a worldwide soil-borne disease of melon (Cucumis melo L.). The most effective control measure available is the use of resistant varieties. Resistance to races 0 and 2 of this fungal pathogen is conditioned by the dominant gene Fom-1. An F₂ population derived from the ‘Charentais-Fom1’ × ‘TRG-1551’ cross was used in combination with bulked segregant analysis utilizing the random amplified polymorphic DNA (RAPD) markers, in order to develop molecular markers linked to the locus Fom-1. Four hundred decamer primers were screened to identify three RAPD markers (B17₆₄₉, V01₅₇₈, and V06₁₀₉₂) linked to Fom-1 locus. Fragments amplified by primers B17₆₄₉ and V01₅₇₈ were linked in coupling phase to Fom1, at 3.5 and 4 cM respectively, whereas V06₁₀₉₂ marker was linked in repulsion to the same dominant resistant allele at 15.1 cM from the Fom-1 locus. These RAPDs were cloned and sequenced in order to design primers that would amplify only the target fragment. The derived sequence characterized amplified region (SCAR) markers SB17₆₄₅ and SV01₅₇₄ (645 and 574 bp, respectively) were present only in the resistant parent. The SV06₁₀₉₂ marker amplified a band of 1092 bp only in the susceptible parent. These markers are more universal than the CAPS markers developed by Brotman et al. (Theor Appl Genet 10:337–345, 2005). The analysis of 24 melon accessions, representing several melon types, with these markers revealed that different melon types behaved differently with the developed markers supporting the theory of multiple, independent origins of resistance to races 0 and 2 of F.o.m.     

OMNICROP – an integrated systems alternative to ideal crop site localization and cultivation chamber self-management utilizing machine learning

OMNICROP uses a database composed of labeled data, such as light quality and quantity, general climate characteristics, and soil quality, from successful farming sites to sort and select the most successful crops for a particular set of circumstances. This process provides either earthbound farmers or off-world colonists with the a priori information needed to start successful, productive food production while preventing costly and time-consuming activities that derive from on-site experimentation. The model can also be directly linked to self-managing cultivation chambers, food seedling physiology assessment, and phytopathology treatment on Earth, and for deep space travel crop cultivation. Our results are derived from the comparison between five different algorithms, showing in this case the superiority of the algorithms based on ensemble of decision trees, especially the boosted trees, where our best estimator was the XGBoost. This project is an open source model where any user can input data and obtain results. Frequent reuse will assist the model with learning and continual self- recalibration, providing increasingly accurate results across time.     

Influence of time of day on measurement with chlorophyll meters and canopy reflectance sensors of different crop N status

Precision Agriculture - Optical sensors are a promising approach for assessing nitrogen (N) status of vegetable crops. However, their potential may be undermined if time of day influences...