Biofilm Formation and Heat Stress Induce Pyomelanin Production in Deep-Sea Pseudoalteromonas sp. SM9913

Pseudoalteromonas is an important bacterial genus present in various marine habitats. Many strains of this genus are found to be surface colonizers on marine eukaryotes and produce a wide range of pigments. However, the exact physiological role and mechanism of pigmentation were less studied. Pseudoalteromonas sp. SM9913 (SM9913), an non-pigmented strain isolated from the deep-sea sediment, formed attached biofilm at the solid–liquid interface and pellicles at the liquid–air interface at a wide range of temperatures. Lower temperatures and lower nutrient levels promoted the formation of attached biofilm, while higher nutrient levels promoted pellicle formation of SM9913. Notably, after prolonged incubation at higher temperatures growing planktonically or at the later stage of the biofilm formation, we found that SM9913 released a brownish pigment. By comparing the protein profile at different temperatures followed by qRT-PCR, we found that the production of pigment at higher temperatures was due to the induction of melA gene which is responsible for the synthesis of homogentisic acid (HGA). The auto-oxidation of HGA can lead to the formation of pyomelanin, which has been shown in other bacteria. Fourier Transform Infrared Spectrometer analysis confirmed that the pigment produced in SM9913 was pyomelanin-like compound. Furthermore, we demonstrated that, during heat stress and during biofilm formation, the induction level of melA gene was significantly higher than that of the hmgA gene which is responsible for the degradation of HGA in the L-tyrosine catabolism pathway. Collectively, our results suggest that the production of pyomelanin of SM9913 at elevated temperatures or during biofilm formation might be one of the adaptive responses of marine bacteria to environmental cues

Spatial Properties of Soil Physical Quality Index S in Black Soil Croplands under Permanent Gully Erosion

Soil physical quality (SPQ) is a limiting factor affecting crop production. However, the impact of gully erosion on the SPQ index S, defined by Dexter as the inflection point of the soil water retention curve (SWRC), remains unclear, especially when considering different latitudinal regions. This study aimed to apply Dexter’s S-theory to evaluate the distribution of index S in black soils adjacent to various gully positions and investigate its relationship with bulk density (Bd), soil organic matter (SOM), and particle percentage. Soil properties (SWRC, Bd, SOM, and particle percentage) from nine gullies in croplands in three latitudinal regions (Harbin, Hailun, and Nenjiang in Heilongjiang province) were determined at the gully edge (GE0) and 50 m beyond the edge into the croplands (GE50) at the following gully units: head, mid-upper, middle, mid-lower, tail, and conjunctions between main gully and gully branch. The S-index was calculated using parameters such as n, θs, and θr, with SWRC data fitted into the van Genuchten model. The results showed spatial variations in the S-index across latitudinal regions, with slightly higher S-values in Harbin than in Hailun and Nenjiang. The S-index also showed noticeable differences at GE0 and GE50 and at the junctions between the main gully and its branches. Approximately 51% of the samples at GE0 and 28.2% of the samples at GE50 had S-values below 0.035, which Dexter proposed as the boundary between good and poor SPQ, indicating a degradation of SPQ at the gully-surrounding areas. A decreased S-index in the gully vicinity was significantly (p −3 for GE0 and GE50) and decreased SOM (36.80 vs. 39.36 g kg−1 for GE0 and GE50). In summary, this study indicates that gully erosion affects the farmland S-index at the gully-surrounding areas through SOM and Bd. Accordingly, measures suited to the increase in the S-index of the gully-surrounding areas may be implemented to maximize the crop yield of farmlands

HTS-PEG: A Method for High Throughput Sequencing of the Paired-Ends of Genomic Libraries

National Natural Science Foundation of China [30730089, 30801012, 31171193]; National Basic Research Program of China (973 Program) [2011CB946101, 2007CB815800]; Fundamental Research Funds for the Central Universities; State High-Tech Development Project (863 Project) [2008AA092601]Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long pairedends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms

The workflow of data processing.

<p>The raw data were first filtered with the hairpin adaptor; reads without hairpin adaptor sequences were discarded. Then the vector sequences of the remaining reads were trimmed. The reads were then divided into left and right ends, and those reads with either end length less than 40 nt were discarded. The filtered paired-end reads were clustered and mapped to the genome.</p

Span distribution of the non-redundant read pairs mapped to the Chinese amphioxus genome.

<p>Span distribution of the non-redundant read pairs mapped to the Chinese amphioxus genome.</p

Increasing tendency of non-redundant read pairs.

<p>50,000, 100,000, 150,000, 200,000, 250,000, 300,000 and 350,000 read pairs were randomly selected and clustered, and three replicates were made at each sampling size. Blue line represents the observed number of cluster, while red line represents its trend. And green line represents the number of increased cluster.</p

Flow chart illustrating HTS-PEG.

<p>The plasmids of the genomic library were sheared to yield fragments of 100–1500 bp larger than the vector (Blue). Then, the EcoR I sites were methylated and hairpin adaptors (Red) which contain non-methylated EcoR I sites were ligated to the fragment ends. After EcoR I digestion and circularization, the paired ends can be amplified by primers that are complementary to the ends of the vector. The PCR products with the desired size can be sequenced using the high-throughput sequencing method.</p