This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V
a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO<
sub>
2<
/sub>
-C and N<
sub>
2<
/sub>
O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, <
i>
Actinobacteria<
/i>
(31.5%), <
i>
Planctomycetes<
/i>
(12.3%), <
i>
Deltaproteobacteria<
/i>
(12.3%), <
i>
Alphaproteobacteria<
/i>
(12.0%) and <
i>
Betaproteobacteria<
/i>
(11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for <
i>
Acidobacteria<
/i>
, <
i>
Actinobacteria<
/i>
, <
i>
Gammaproteobacteria<
/i>
and <
i>
Verrucomicrobia<
/i>
with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for <
i>
Gammaproteobacteria<
/i>
. <
i>
Actinobacteria<
/i>
were more responsive to straw retention with <
i>
Rubrobacterales<
/i>
, <
i>
Bifidobacteriales<
/i>
and <
i>
Actinomycetales<
/i>
related to the chemical factors of N+V-amended soils. <
i>
Acidobacteria<
/i>
subgroup 7 and <
i>
Opitutae<
/i>
, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO<
sub>
2<
/sub>
-C and N<
sub>
2<
/sub>
O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as <
i>
Acidobacteria<
/i>
, <
i>
Actinobacteria<
/i>
and <
i>
Verrucomicrobia<
/i>
, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors.