Table 3.

A summary of microbial community compositional and functional studies on temporary streams and general relationships established.

Citation	Study system	Microbial community metric(s)	Microbial functional metric(s)	Primers or probes used	Summary of results
Amalfitano et al., 2008	Mulargia River (Sardinia, Italy), River Krathis (Peloponnesus, Greece), River Pariela (Portugal), River Tagliamento (Italy).	Bacterial abundance and biomass: DAPI; Community composition: Fluorescence in-situ hybridization (FISH), Automated ribosomal intergenic spacer analysis (ARISA).	Bacterial production ([3-H]leucine incorporation).	Probes: ARCH915, EUB338, EUB338-II, ALF1b, BET42a, GASM42a, PLA46a, CF319a, HGC69a, LGC354abc.	Following experimental desiccation, bacterial carbon production and biomass decreased strongly. Limited change in community structure with increase in Alphaproteobacteria and Betaproteobacteria with drying.
Frossard et al., 2012	Terrestrial soils, ephemeral and permanent stream channel sites in the Chicken Creek watershed (Germany).	Community composition: Denaturing gradient gel electrophoresis (DGGE).	Extracellular enzyme activity: Phosphatase, β-glucosidase, β-xylosidase, cellobiohydrolase, chitinase, leucine-aminopeptidase, aspartate-aminopeptidase, glutamate-aminopeptidase, phenol oxidase, phenol perioxidase.	Primers: Eub338f/Eub518r	Bacterial community structure did not show differences between permanent and ephemeral stream sediments. Enzyme activity was seasonally variable but was not related to microbial community composition.
Febria et al., 2012	In-stream colonization corers at 1 permanent and 1 temporary headwater stream (Ontario, Canada).	Community composition: 16S T-RFLP.		Primers: 27F/1492R.	Strong temporal differences in hyporheic porewater community structure both before and after a drying event
Fierer et al., 2003	Soils from Sedgwick Ranch Natural Reserve (Santa Ynez, CA, USA).	Community composition: 16S terminal restriction fragment length polymorphism (T-RFLP).		Primers: 8 F hex/1389R.	During experimental drying/wetting cycles community composition was varied by environment. Soils without less history of moisture stress, but not in soils with a history of moisture stress.
Frossard et al., 2013	Succession of microbial community in flumes filled with dry stream bed sediments from the Chicken Creek watershed (Germany).	Community composition: ARISA	Extracellular enzyme activity: Phosphatase, β-glucosidase, β-xylosidase, cellobiohydrolase, chitinase, leucine-aminopeptidase, aspartate-aminopeptidase, glutamate-aminopeptidase, phenol oxidase, phenol perioxidase.	Primers: 1406F-FAM/23Sr.	Strong temporal differences in community structure during succession experiments. Enzyme activity changes were linked to shifts in microbial community structure.
Manis et al., 2014	Survey of known temporary streams in agricultural landscapes (USA).	Community composition: 16S and nosZ T-RFLP and 16S and nosZ quantitative polymerase chain reaction (qPCR). Community abundance: DAPI fluorescence microscopy.	Dentrification enzyme assays.	16S T-RFLP Primers: Eub338F-0-III, Eub338F-I-II/1392R. 16S qPCR Primers: Eub339, Eub339 II/ Eub518. nosZ T-RFLP Primers: nosZ-F-1181/nosZR. nosZ qPCR: nosZ1F/nosZ2R.	Greater denitrification rates were observed in ephemeral vs. perennial channels, but potential denitrification was not correlated to denitrifier abundance.
McIntyre et al., 2009	Barnett Creek (Pilbara region, Western Australia). Ephemeral stream located in lowland floodplain.	Microbial biomass: phospholipid fatty acid (PLFA) analysis.	Carbon mineralization assay; carbon dioxide flux assay; carbon and nitrogen stable isotopes.		Landscape position (e.g., riparian soils, floodplain soils, and channel sediments) was less important to microbial activity than soil saturation once water content was greater than 40%. Mineralization of carbon and nitrogen occurs more slowly following complete saturation of sediments compared to brief events that rapidly stimulate microbial activity.
Rees et al., 2006	Semi-permanent stream near Binalong, New South Wales, Australia	Community composition:16S T-RFLP.		Primers: 27F/1492R.	Community composition varied by hydrological condition and within riffles. Communities were changed after drying and did not recover to pre-drought conditions one month after flow was restored.
Timoner et al., 2014a	Dam Creek (South-East Queensland, Australia). First order intermittent headwater stream.	Bacterial abundance: fluorescence microscopy.	Microbial carbon degradation: BiologEcoPlates.		Before re-wetting biofilms differed based on time since drying. Rewetting rapidly increased biofilm functional diversity and functional patterns became more similar across sites. Low counts of bacteria were found in both wet and dry isolated pools in an intermittent channel.
Timoner et al., 2014b	Fuirosos temporary stream (Spain).	Community composition: 16S pyrosequencing.		Primers: 28F/519R.	Differences between biofilm, shallow streambed hyporheic bacterial communities related to flow, drying stress/desiccation and sediment type.
Timoner et al., 2014c	Fuirosos (Iberian Peninsula, Spain). Third order temporary stream.	Community structure and abundance: Chlorophyll-a concentration, pigment composition.			Chlorophyll-a concentrations went down in response to drying but quickly returned following re-wetting. Tendency toward production of protective carotenoids and desiccation resistance structures (e.g., increased membrane thickness and spore production) during drying.
Zeglin et al., 2011	Onyx River (McMurdo Dry Valleys, Antarctica); Rio Salado (New Mexico, USA). Both ephemeral desert streams.	Community composition: DGGE, Clone library analysis.		Primers: 8F/1391R or 1492R. 519R, 515F, 1100R, and 1492R.	Bacterial diversity at both sites was not correlated with sediment water content but was instead most strongly related to conductivity. Community composition was strongly related to water content.
Zoppini et al., 2010	Mulargia River (Sardinia, Italy). Second-order temporary river.	Bacterial abundance/community composition: FISH, DAPI fluorescence microscopy.	Bacterial production ([3-H]leucine incorporation); extracellular enzyme activity.	Probes: EUB338, EUB338-II, EUB338-III, ALF968, BET42a, GAM42a, CF319a, PLA46a, and LGC354abc.	Metrics including bacterial cell counts, bacterial productivity, and enzyme activity were largely comparable during wet and dry conditions. Community composition was not substantially different between wet and dry conditions. Enzyme activities increased during flooding event.
Febria et al. (This study)	Speed River system, Ontario, Canada.	Community composition: 16S T-RFLP.		Primers: 27F/1492R.	Similar community composition in sediment between sites, highly varied surface water communities.
Febria et al. (This study)	Parkers Creek system, Maryland, USA.	Community composition: 16S Illumina MiSeq.		Primers: 515F/806R.	Community composition similar by site. Seasonal changes in microbial community composition were not linked to flow status.