Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

Abstract

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley

“…Soil DNA kit (Omega Bio-Tek, Norcross, GA, USA) following the manufacturer’s instructions. The bacterial V3-4 region was then amplified with the primer set 338F (5′-ACT CCT ACG GGA GGC AGC AG-3′) and 806R (5′-GGA CTA CHV GGG TWT CTA AT-3′) ( Zeng & An, 2021 ). PCR amplification and purification were performed following previously described methods ( Yang, Liu & Zhang, 2019 ).…”

Probiotic Effects of Lactobacillus fermentum ZJUIDS06 and Lactobacillus plantarum ZY08 on Hypercholesteremic Golden Hamsters

“…Quantity and quality of the extracted DNA were measured using the NanoDrop DN-1000 spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, USA) and agarose gel electrophoresis, respectively. PCR amplification of the bacterial 16S rRNA genes V3-V4 region was performed using the forward primer 338F ( 5′ -ACTCCTACGGGAGGCAGCA-3 ′ ) and the reverse primer 806R ( 5′ -GGACTACHVGGGTWTCTAAT-3 ′ ) (Personal Biotechnology Co. Ltd., Shanghai, China) (42)(43)(44). Sample-specific 7-bp barcodes were added to the primers for multiplex sequencing.…”

Cover Cropping Impacts Soil Microbial Communities and Functions in Mango Orchards

“…The soil bacterial community was determined by sequencing hypervariable V3-V4 regions of 16S rRNA genes using primers 338F (ACTCCTACGGGAGGCAGCA) and 806R (GGACTACHVGGGTWTCTAAT) [27]. The PCR amplification conditions for 16S rRNA were 50 s at 94 • C, 30 s at 40 • C, 35 cycles of 60 s at 72 • C, followed by 5 min at 72 • C [28]. The ITS1 variable region was sequenced with primer sets ITS3 (5 -GCATCGATGAAGAACG-CAGC-3 ) and ITS4 (5 -TCCTCCGCTTATTGATATGC-3 ) [29,30] to assess the soil fungal community.…”