Divergent Responses of Forest Soil Microbial Communities under Elevated CO ₂ in Different Depths of Upper Soil Layers

Abstract

Numerous studies have shown that the continuous increase of atmosphere CO concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO (eCO) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO at both soil depths, although the stimulation effect of eCO on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO increases. The concentration of atmospheric carbon dioxide (CO) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO (eCO) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers

“…The decrease of soil total carbon has been observed not only in this PHACE site, but also in an agricultural FACE site ( Xiong et al, 2015 ). The total signal intensities of mcrA and pmoA genes were significantly enhanced under eCO 2 , which is in agreement with previous studies of forest and agricultural FACE sites ( Xiong et al, 2015 ; Yu et al, 2018 ). The methane production may be stimulated under eCO 2 , which could enhance methane uptake by increasing substrate availability for the methanotrophs.…”

“…A study of this PHACE experimental site showed a positive feedback of microbial communities under eCO 2 ( Nie et al, 2013 ), while other reports showed that eCO 2 has no significant response ( Sinsabaugh et al, 2003 ; Austin et al, 2009 ) at the FACE site. Additionally, several previous studies showed that key genes involved in C degradation, C fixation, and methane metabolism cycling were stimulated under eCO 2 in grassland, agricultural, and forest ecosystems ( He et al, 2010b ; Xiong et al, 2015 ; Yu et al, 2018 ). These results appear consistent with the present study, using the same GeoChip technology, revealing that the abundances of most of the functional gene involved in C cycling were significantly enhanced under eCO 2 .…”

“…At this experimental site the composition and phylogenetic and functional structures of soil microbial communities were dramatically altered under warming, eCO 2 , and eCO 2 + warming. Previous studies have shown that microbial community structure shifted under eCO 2 ( He et al, 2010b , 2014 ; Yu et al, 2018 ) and warming ( Sheik et al, 2011 ; Xue et al, 2016a , b ). Our results agreed with these reports, which were supported by both the Adonis and DCA analysis of all detected genes.…”

“…DNA quality was measured using an ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, NC, United States) to determine 260/280 nm and 260/230 nm ratios, and DNA concentration was quantified with Quant-It PicoGreen (Invitrogen, Carlsbad, CA, United States). Approximately 3 μg purified DNA per sample was labeled with the fluorescent dye Cy-5 (GE Healthcare) using a random priming method ( He et al, 2014 ; Yu et al, 2014b , 2018 ).…”

“…A high-throughput functional gene array (GeoChip 3.0) ( He et al, 2010a ) was employed to analyze the soil microbial communities in the above mentioned semiarid grassland experimental site. GeoChip 3.0 contains approximately 28,000 oligonucleotide probes involved in many biogeochemical functional processes [such as C, N, sulfur (S) and phosphorus (P) cycling], and has been used to examine the microbial communities from various environments ( Yu et al, 2014a ; Cai et al, 2015 ; Xiong et al, 2015 ; Xue et al, 2016a ; Yu et al, 2018 ). In this study, we attempted to address whether (i) the functional composition and structure of soil microbial communities would be dramatically altered as soil C inputs and soil properties change in response to multiple climate factors; (ii) soil microbial functional processes (e.g., C and N cycling) would have different responses to warming, eCO 2 and the interaction between these two factors.…”