Nutrient resource availability is a crucial environmental factor in determining soil bacterial community assembly. However, the effects of nutrient availability on niche differentiation and temporal co-occurrence patterns of bacterial communities remain elusive. Here, we retrieved sequencing datasets (105 amplicon samples of bacterial 16S rRNA genes and 60 bacterial metagenomic samples) from a laboratory incubation experiment and a coastal wetland study, to elucidate the effects of nutrient availability on niche differentiation and co-occurrence patterns of bacterial communities. Niche differentiation within bacterial communities, indicated by nearest taxon index and niche breadth of bacterial communities, did not significantly correlate with nutrient availability gradients in either environment, even though deterministic processes dominated bacterial community assembly. Network analyses revealed that co-occurrence patterns of bacterial OTUs over incubation time changed across nutrient availability gradients, and were likely to be mediated by environmental selection. There were more co-occurrences of metabolic genes under higher nutrient levels. This study revealed the non-significant correlation between nutrient availability gradients and niche differentiation within bacterial communities, not only in a natural environment but also in a laboratory modified environment where the nutrient availability gradient was the sole environmental variable. These findings boost the understanding of bacterial community assembly along environmental nutrient availability gradients.