The　dynamic　changes　of　soil　microorganisms　after　Phragmites　australis　straw　addition　in　the　incubation　tubes　were　analyzed　by　phospholipid　fatty　acid　stable　isotope　probing　(PLFA-SIP).　After　comparing　soils　from　different　freshwater　pumping　areas　in　the　Yellow　River　Estuary　(10-year　pumping　area,　15-year　pumping　area　and　natural　salt　marsh　without　pumping),　the　results　showed　that　the　total　PLFA　contents　significantly　increased　by　59.99%–146.93%　after　the　addition　of　straw　to　surface　soils　(0–10　cm)　in　the　pumping　areas,　whereas　the　changes　in　deeper　soils　(10–20　cm)　were　not　significant.　In　particular,　the　PLFA　results　showed　that　bacteria　and　fungi　were　significantly　increased　after　10　days　with　straw　addition.　Straw　treatment　also　improved　the　ratio　of　fungi　to　bacteria　(F:B)　in　the　surface　soils　of　all　sampling　sites.　The　soil　microorganisms　directly　absorbed　straw-derived　13C,　where　Gram-negative　bacteria　(GN)　were　found　to　have　the　highest　PLFA-13C　values　during　the　40-day　decomposition　process.　Soil　characteristics　can　significantly　affect　microbial　community　composition.　Accordingly,　soil　organic　carbon　(SOC)　was　found　to　be　significantly　positively　related　to　bacterial,　fungal　and　other　microbial　biomasses,　while　moisture,　electric　conductivity　(EC)　and　soil　aggregate　composition　were　important　factors　of　influence　on　the　microbial　community.　The　findings　indicated　that　both　fungi　and　bacteria　were　essential　microbial　communities　in　straw　decomposition,　the　significant　increase　of　fungi　biomass　and　the　absorption　of　straw-derived　13C　by　bacteria　were　the　main　changes　of　microbial　community.　Long-term　freshwater　pumping　can　promote　straw　decomposition　by　increasing　microbial　biomass　and　changing　microbial　community　composition.　©　2020　Elsevier　B.V.