Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation

Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems

Targeted identification of genomic regions using TAGdb

Background: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results: We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly

Responses of the soil microbial community to nitrogen fertilizer regimes and historical exposure to extreme weather events : flooding or prolonged-drought

Extreme weather events, including flooding and prolonged-drought, may establish long-lasting effects on soil biotic and abiotic properties, thus influencing ecosystem functions including primary productivity in subsequent years. Nitrogen (N) fertilizer addition often improves soil fertility, thereby potentially alleviating legacy effects on soil function and plant productivity. The soil microbial community plays a central role in mediating soil functioning; however, little is known about the legacy impacts of extreme weather events and N fertilizer addition on soil bacterial communities and the key processes involved in carbon (C) cycling. Here, the potential legacy effects of waterlogging, prolonged-drought and N fertilizer addition (0, 100, 200 and 300 kg N/ha) on soil bacteria and microbial respiration were investigated. The abundance, diversity and composition of the bacterial community, and basal and induced-respiration rates, in a farming soil system were examined, using quantitative PCR, high-throughput DNA sequencing, and MicroResp™. Soils previously exposed to short-term waterlogging events and prolonged-drought (by air-drying for 4 months) were used in our study. Prolonged drought, but not waterlogging, had a strong legacy effect on the soil bacterial community and microbial respiration. The addition of N fertilizer up to 300 kg N/ha could not fully counteract the legacy effects of prolonged-drought on soil bacteria. However, N addition did increase bacterial abundance and diversity, and inhibited soil microbial respiration. Significant correlations between microbial respiration and bacterial community structure were observed, but N addition weakened these relationships. Our results suggest that the resilience (rate of recovery) of soil bacterial communities and functions to prolonged-drought is limited in farming systems, and therefore, may take a long time to recover completely. Subsequently, this should be explicitly considered when developing adaptation strategies to alleviate the impacts of extreme weather events

The pangenome of hexaploid bread wheat

There is an increasing understanding that variation in gene presence–absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene pres- ence–absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 102 genes, a core genome of 81 070 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal sin- gle nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/ gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_ge nome_databases.php

Wheatgenome.info: a resource for wheat genomics resource

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/

Genomic databases for crop improvement

The majority of DNA sequence and expressed gene sequence data generated today comes from the next-or second-generation sequencing (NGS/2GS) technologies. NGS technologies produce vast quantities of short data rather than Sanger sequencing at a relatively low cost and short time. Genomics is undergoing a revolution, driven by advances in DNA sequencing technology, and this data flood is having a major impact on approaches and strategies for crop improvement. NGS technologies have been applied for sequenced genomes of a number of cereal crop species including rice, Sorghum and maize. A quality sequence of rice that covers 95% of the 389 Mb genome has been produced [1]. The Sorghum bicolor (L.) Moench genome has been assembled in size of 730-megabase, placing ~98% of genes in their chromosomal context [2]. The draft nucleotide sequence of the 2.3-gigabase genome of maize has also been improved [3]. One of the challenges encountered by researchers is to translate this abundance of data into improved crops in the field. There remains a gap between genome data production and next-generation crop improvement strategies, but this is being rapidly closed by far sighted companies and individuals with the ability to combine the ability to mine the genomic data with practical crop-improvement skills. Bioinformatics can be defined as the structuring of biological information to enable logical interrogation, and databases are a key part of the bioinformatics toolbox. Numerous databases have been developed for genomic data, on a range of platforms and to suite a variety of different purposes (see Table 1 for examples). These range from generic DNA sequence or molecular marker databases, to those hosting a variety of data for specific species

Genomic databases for crop improvement

The majority of DNA sequence and expressed gene sequence data generated today comes from the next-or second-generation sequencing (NGS/2GS) technologies. NGS technologies produce vast quantities of short data rather than Sanger sequencing at a relatively low cost and short time. Genomics is undergoing a revolution, driven by advances in DNA sequencing technology, and this data flood is having a major impact on approaches and strategies for crop improvement. NGS technologies have been applied for sequenced genomes of a number of cereal crop species including rice, Sorghum and maize. A quality sequence of rice that covers 95% of the 389 Mb genome has been produced [1]. The Sorghum bicolor (L.) Moench genome has been assembled in size of 730-megabase, placing ~98% of genes in their chromosomal context [2]. The draft nucleotide sequence of the 2.3-gigabase genome of maize has also been improved [3]. One of the challenges encountered by researchers is to translate this abundance of data into improved crops in the field. There remains a gap between genome data production and next-generation crop improvement strategies, but this is being rapidly closed by far sighted companies and individuals with the ability to combine the ability to mine the genomic data with practical crop-improvement skills. Bioinformatics can be defined as the structuring of biological information to enable logical interrogation, and databases are a key part of the bioinformatics toolbox. Numerous databases have been developed for genomic data, on a range of platforms and to suite a variety of different purposes (see Table 1 for examples). These range from generic DNA sequence or molecular marker databases, to those hosting a variety of data for specific species.</p

Next-generation sequencing applications for wheat crop improvement

Bread wheat (Triticum aestivum; Poaceae) is a crop plant of great importance. It provides nearly 20% of the world' s daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement