A Comparison of Soils and their Associated Microbial Communities as Affected by Sugarcane Cultivation

In Louisiana, sugarcane has been grown in the same soils for over 200 years. A phenomenon wherein soils with a long-term sugarcane cropping history produce decreased yields compared to adjacent land without a recent history of sugarcane cultivation has been documented in multiple sugarcane growing regions. Research in both Louisiana and internationally has shown positive plant growth responses when soils with a long-term cultivation history are sterilized or treated with selective biocides, suggesting there is a biological component to the underlying soil health issue. In this study, soil microbial ecology was compared for paired sites with short and long-term sugarcane cropping histories at six locations in plant cane and two in plant cane and first ratoon. Yield estimates of paired sites revealed crops grown in short-term cultivation soils generally out-yielded their long-term counterparts. Soil properties that can influence microbial ecology, including soil organic matter, macro and micronutrients, and soil extracellular enzymes, were generally present at higher levels in short-term cultivation soils, but varied by location. Root staining revealed greater fungal endophyte colonization in long-term cultivation soils. Distance-based redundancy analysis of fatty acid methyl ester biomarkers revealed differences in community structure based primarily on location but also cropping history. Analysis of 16S prokaryotic and ITS fungal amplicon-based metagenomic β-diversity data revealed prokaryotic community structure was also primarily influenced by location, whereas fungal communities differed based on cropping history. This suggests fungi are major contributors to the detrimental effects associated with sugarcane monoculture. Additional α-diversity comparisons of 16S and ITS metagenomes revealed portions of prokaryotic and fungal communities were more commonly associated with short and long-term sugarcane cultivation in both bulk and rhizosphere soils. Candidate microorganisms beneficial to sugarcane growth that were more abundant in soils with a short-term cropping history included 107 prokaryotic genera and 37 fungal genera in bulk soils and 97 prokaryotic genera and 46 fungal genera in rhizosphere soils. Candidate microorganisms detrimental to sugarcane growth that were more abundant in soils with a long-term cropping history included 117 prokaryotic genera and 58 fungal genera in bulk soils and 94 prokaryotic genera and 40 fungal genera in rhizosphere soils

A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in <i>Pinus</i> (Pinaceae)

Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences ofycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group

Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)

Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compare interspecific variation between ptSSRs and nucleotide sequences of ycf1 then test intraspecific variation for ptSSRs using 911 samples in the P. ponderosa species complex. Results: The ptSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The ptSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for ptSSR loci in a plastome alignment for the target group

Alignment of 15 cpSSR primer pairs with Pinus plastomes

The published nucleotide sequences for 15 cpSSR primer pairs located within the aligned plastomes of 107 species of Pinus and six Pinaceae outgroups (TreeBase S12640)