The effect of nutrient additions on bacterial activity in seagrass (Posidonia oceanica) sediments

The influence of nutrient additions on benthic bacterial activity under seagrass meadows was tested by enriching five seagrass (Posidonia oceanica) meadows with nutrients over one year. We found a highly significant response of benthic bacterial activity to nutrient additions, which was reflected in greater (about two-fold) ammonification rates and, to a smaller extent, a significant tendency for a greater exoenzymatic activity. Nutrient additions significantly raised bacterial activity, without altering the seasonal changes in bacterial activity. As a result of the increased bacterial activity, the organic content of the sediments declined significantly, by about 33%, after one year of nutrient addition. Hence, nutrient additions to the seagrass meadows enhance seagrass production but also accelerate bacterial decomposition of seagrass carbon, thereby reducing the capacity of the sediments to store organic carbon. These results demonstrate that sediment nutrient availability limits bacterial activity in these Posidonia oceanica meadows, and identify bacteria as important nutrient consumers in these systems.     

The effects of manipulation of sedimentary iron and organic matter on sediment biogeochemistry and seagrasses in a subtropical carbonate environment

The microbial metabolism of organic matter (OM) in seagrass beds can create sulfidic conditions detrimental to seagrass growth; iron (Fe) potentially has ameliorating effects through titration of the sulfides and the precipitation of iron-sulfide minerals into the sediment. In this study, the biogeochemical effects of Fe availability and its interplay with sulfur and OM on sulfide toxicity, phosphorous (P) availability, seagrass growth and community structure were tested. The availability of Fe and OM was manipulated in a 2 × 2 factorial experiment arranged in a Latin square, with four replicates per treatment. The treatments included the addition of Fe, the addition of OM, the addition of both Fe and OM as well as no addition. The experiment was conducted in an oligotrophic, iron-deficient seagrass bed. Fe had an 84.5% retention efficiency in the sediments with the concentration of Fe increasing in the seagrass leaves over the course of the experiment. Porewater chemistry was significantly altered with a dramatic decrease in sulfide levels in Fe addition plots while sulfide levels increased in the OM addition treatments. Phosphorus increased in seagrass leaves collected in the Fe addition plots. Decreased sulfide stress was evidenced by heavier δ³⁴S in leaves and rhizomes from plots to which Fe was added. The OM addition negatively affected seagrass growth but increased P availability; the reduced sulfide stress in Fe added plots resulted in elevated productivity. Fe availability may be an important determinant of the impact that OM has on seagrass vitality in carbonate sediments vegetated with seagrasses.     

Fish farming impact on decomposition of Posidonia oceanica litter

Fish farming impact on decomposition and loss of carbon, nitrogen and phosphorus fixed in seagrass litter were studied in a Posidonia oceanica meadow (Aegean Sea, Greece) using in situ incubation of senescent seagrass leaves collected under (station: cages) and away (station: control) from fish cages and deployed in a cross design of origin/station. Decomposition rate and loss of carbon and nitrogen fixed in seagrass litter were pronounced under the cages while loss of phosphorus was less evident. Decomposition was related to nutrient availability in seagrass tissue and pore water, sediment organic matter and origin of seagrass litter. When incubated under the cages, litter originated from the control decomposed faster than litter originated from the cages since the former was qualitatively better substrate for decomposers and the nutrient conditions in that station were enriched in the pore water and sediment. The lower decomposition of litter originated from cages suggests that seagrass tissues under the cages accumulate chemical deterrents, possibly in order to confront high grazing pressure, which on the other hand reduces the rate of decomposition.     

Seasonal fluxes of O2, DIC and CH4 in sediments with Vallisneria spiralis: indications for radial oxygen loss

Seasonal fluxes of dissolved oxygen, inorganic carbon and methane were measured in microcosms containing vegetated (Vallisneria spiralis L.) and unvegetated sediments under controlled laboratory conditions. We tested if measured fluxes were affected by a moderate (6% as loss on ignition, LOI) and an elevated (10%) organic matter content (OM) in sediments. Microcosms were set up with plants and sediments collected from two riverine sites, upstream (moderate OM load) and downstream (elevated OM load) of a wastewater treatment plant. Light and dark fluxes were measured and V. spiralis net primary production and respiration rates were calculated. Unvegetated sediments were always net heterotrophic and behaved as methane sources to the water column, with significantly higher CH₄ release during summer from sediment with elevated OM load. Vegetated sediments were always net autotrophic with attenuated or negative CH₄ fluxes, suggesting the occurrence of processes within the rhizosphere that inhibit methane production or favor its oxidation. Vegetated sediments had an unbalanced O₂ to DIC stoichiometry, with average photosynthetic quotients varying between 0.30 and 0.68, significantly below one. The missing oxygen amount varied seasonally, with a minimum in the summer coinciding with the highest water temperature, but was not dependent upon the two OM levels. Overall these results suggest that V. spiralis is likely to transport a significant proportion of photosynthetically produced oxygen to the rhizosphere.     

Causes of sulfur isotope variability in the seagrass, Zostera capricorni

Sulfur has been proposed as a useful element to employ in addition to carbon and nitrogen in stable isotope studies of marine food webs, but variability in δ³⁴S of primary producers may prevent food web resolution. δ³⁴S values in green leaves of the seagrass, Zostera capricorni, showed considerable variability (12.7-17.6‰) in a survey in Moreton Bay, Australia. We demonstrated that δ³⁴S values were correlated with sediment organic matter (OM) content and height of seagrass on the tidal gradient, but these relationships were opposite to those expected from work elsewhere. In our survey, δ³⁴S values were relatively depleted at sites higher on the shore and with lower OM content. We did find the expected relationship of depleted δ³⁴S values where sediment porewater sulfide concentrations were higher. Any influence of OM content on δ³⁴S values would have been confounded in the survey by the relationship between height on shore and OM content itself. We separated the effects of height and OM content by creating the following treatments at one height on the shore: (1) OM added, (2) procedural control, and (3) untouched control. δ³⁴S values of seagrass in OM added plots were significantly depleted (5.6‰) relative to procedural (10.1‰) and untouched (11.0‰) controls 8 weeks after the manipulation. This demonstrated that OM content on its own does have the expected effect on δ³⁴S values of seagrass, so in the initial survey another factor, probably related to height on shore, must have overridden the influence of OM content. Seagrass roots are able to exude excess oxygen produced during photosynthesis, reoxidising sulfides in surrounding porewater. We demonstrated that the above and below-ground biomass of seagrass was higher low on the shore, and contend that higher seagrass productivity low on the shore results in greater reoxidation of sulfides and leads to more enriched δ³⁴S values of seagrass.     

Dissolved and particulate organic matter in contrasting Zostera marina (eelgrass) sediments

The influence of seagrass Zostera marina on sediment characteristics was examined in two contrasting sediments, one organic-rich and one organic-poor. The presence of plants leads to reduced sediment redox potential in both sediment types compared to bare sediment with the largest effects in the organic-poor sediment. Z. marina stimulated the sulfate reduction rates in organic-poor sediment with ∼50% and higher pools of dissolved organic carbon (DOC) were found. In contrast, sulfate reduction rates were lower in vegetated compared to bare sites in the organic-rich sediment. Despite a low contribution of dissolved carbohydrate (DCHO) to the DOC pool (<5%), the seagrass vegetation was responsible for an increase of ∼50% in DCHO pools with a peak in the root zone suggesting that Z. marina supplied DCHO to the pore waters. The Z. marina meadows also enhanced the contribution of particulate carbohydrate (PCHO) to sedimentary particulate organic carbon (POC) pools by 6-14% compared to bare sediment. Although the PCHO pools were higher in organic-rich than organic-poor sediments, the analyses of carbohydrate composition revealed that three groups of neutral sugars including glucose, galactose and mannose+xylose were the major compounds of PCHO and contributed with >60% to sedimentary carbohydrate pools at both sites. Only glucose showed depletion with depth in the vegetated sediments, whereas the percentage of ribose and rhamnose increased indicating a selective degradation of labile carbohydrates in the meadows. Galactose and mannose+xylose appeared to represent a refractory part of carbohydrate that remained after degradation of the more labile components. The sugar content was rather constant with depth at the bare organic-rich sediment indicating that only recalcitrant carbohydrate pools were buried. There was less difference in the PCHO composition profiles between vegetated and bare organic-poor sediments.     

Effects of nitrogen addition on nitrogen metabolism and carbon reserves in the temperate seagrass Posidonia oceanica

The effect of repeated N additions on a dense, shallow meadow of Posidonia oceanica (L.) Delile in the NW Mediterranean was studied over a year. N was added biweekly both to the sediment and to the water column as ammonium and nitrate. The most obvious result of these additions was an overall increase in N content (% DW) in all tissues of fertilized plants; this increase was maximum in rhizomes, with values of 5% N reached, which confirmed the storage capacities of these organs.Fertilization affected the different N fractions in distinct ways. The free amino acid (FAA) concentration increased the most, particularly in rhizomes and roots, suggesting the function of these compounds for N storage and, probably, translocation. The non-soluble N fraction also increased greatly. The total soluble protein (TSP) and the inorganic N forms concentrations were less sensitive to fertilization, and only increased moderately in a few cases. N assimilation, assessed through in vivo glutamine synthetase (GS) activity, was maximum in leaves after the peak of growth, which coincided with the lowest N values in both control and fertilized plants. Thus assimilation was probably greatest at the period of highest N deficiency. Growth rates did not respond to N enrichment. Another clear effect of N addition was to decrease carbon reserves. In effect, the concentration of total non-structural carbohydrate (TNC) greatly decreased in rhizomes of fertilized plants, coinciding with the increase in FAA. We conclude that increased nitrogen availability can affect plant survival through the decrease in their carbon reserves, crucial for P. oceanica overwintering. This interaction between N and C metabolism helps to explain changes in benthic vegetation after steadily increasing coastal water eutrophication.     

Response of Benthic Protozoa and Thraustochytrid Protists to Fish Farm Impact in Seagrass (Posidonia oceanica) and Soft-Bottom Sediments

We investigated the impact of fish farm biodeposition on benthic bacteria, thraustochytrid protists, and heterotrophic protozoa (nanoflagellates and ciliates) in an oligotrophic area of the Mediterranean Sea. The fish farm impact was investigated both on a seagrass (Posidonia oceanica) bed and on soft bottom sediments. In both systems, sediment samples were collected with a multicontrol sampling strategy (i.e., beneath the fish farm and at three control sites per system). The uneaten food pellets supplied to the fish determined the accumulation of sediment organic matter and the enhancement of protein content in impacted sediments (both seagrass bed and soft sediments). In both systems, the abundance and biomass of heterotrophic protists increased significantly beneath the fish farm, but the structure of the protist assemblages responded differently in vegetated and unvegetated sediments. Thraustochytrid abundance increased significantly in impacted seagrass. These results provide evidence that the structure of protist assemblages respond significantly to fish farm biodeposition and indicate that the monitoring of these benthic components provides complementary information for the assessment of the fish farm impact on the benthic systems.     

The effect of wrack composition and diversity on macrofaunal assemblages in intertidal marine sediments

Wrack (dead, washed-up seaweed and seagrass) buried in soft substrata may increase the organic content and alter the physical structure of sediments. These effects may influence the composition and structure of macrofaunal assemblages in the sediment. Such influences can be expected to vary according to the type and amount of wrack as well as the presence of invasive seaweeds in the wrack. In this study, we deliberately buried different amounts of the invasive species Sargassum muticum in isolation or mixed to the native species Ulva sp. and Fucus vesiculosus, in two intertidal sandflats to test some hypotheses about the response of macrofaunal assemblages. We tested whether (1) diversity of detritus (i.e. different mixtures), and (2) the amount of detritus of S. muticum influenced the composition and the relative abundance of macrofaunal assemblages. We also assessed whether the sediment organic carbon and the biomass of benthic microalgae varied depending on the diversity of detritus and the amount of detritus of S. muticum. Finally, we tested if these effects of wrack were consistent across sites. Results indicated that buried wrack affected the composition and structure of macrofaunal assemblages in short-term (i.e. 4 weeks), but there were no differences depending on detritus diversity or the amount of S. muticum. In addition, sediment organic matter and microalgal biomass were not affected by the addition of wrack. They instead varied greatly among small spatial scales (i.e. plots). Wrack composition or abundance of the invasive species S. muticum played thus a small role in shaping the structure of macrofaunal assemblages or the biomass of benthic microalgae in these intertidal sediments, probably because these sediments are frequently affected by various inputs of organic matter and benthic assemblages are already adapted to organically enriched sediments.     

Effect of increased sediment sulfide concentrations on the composition of stable sulfur isotopes (δS) and sulfur accumulation in the seagrasses Zostera marina and Posidonia oceanica

The effect of increased sediment sulfide concentrations on the sulfur isotopic composition (δ³⁴S), total sulfur (TS) and elemental sulfur (S⁰) concentrations in plant tissues was studied for the two seagrasses Zostera marina (3 weeks in laboratory) and Posidonia oceanica (4 months in situ). Porewater sulfide concentrations were experimentally regulated and plants exposed to high sediment sulfide concentrations had δ³⁴S signals closer to the δ³⁴S of sulfide, whereas plants exposed to no / low sulfide concentrations had δ³⁴S signals closer to the δ³⁴S of seawater sulfate, indicating a higher sulfide invasion in plants exposed to high sulfide concentrations. The δ³⁴S varied between the plant tissues in both species with the leaves having more positive δ³⁴S signals than roots and rhizomes, indicating that sulfide was invading into the roots and moved to the other tissues through the lacunae. TS and S⁰ concentrations were higher in plants exposed to sulfide in both experiments suggesting that sulfur derived from sediment sulfide accumulated in the plants. The δ³⁴S signal in S⁰ was similar to sediment sulfide verifying that S⁰ found in the seagrasses originated from sediment sulfide. Direct comparisons of δ³⁴S in the two different seagrasses and across the treatments were not possible due to large differences in δ³⁴S of the sulfur sources. F_sulfide adjusted for these differences and may be a useful alternative, when δ³⁴S of the sulfur sources varies between study sites. There were no significant effects of sulfide exposure on plant growth and mortality in Z. marina and P. oceanica after 3 weeks and 8 weeks exposure, respectively, but P. oceanica showed indications of reduced growth and higher mortality after 16 weeks of sulfide exposure probably due to sulfide invasion/toxicity.     

Small-scale burial of macroalgal detritus in marine sediments: Effects of Ulva spp. on the spatial distribution of macrofauna assemblages

Patches of dead seaweeds can deposit, bury, and age into the sediment. Decomposition and release of algal-derived nutrients can influence patterns of distribution of benthic organisms. Here, I investigated how small-scale burial of Ulva spp. affected spatial variation of macrofauna in intertidal sediment. I deliberately buried Ulva detritus under the surface of 50 × 50 cm² patches of sediment in three intertidal flats of the Oosterschelde estuary (The Netherlands). Results showed that there was no accumulation of particulate organic carbon and nitrogen in the sediment at the scales examined. The biomass of microphytobenthos did not show any change and there was evidence that grazing was important all over the study area. Burial did not alter composition and diversity of macrofauna, but some animals (Corophium volutator, Eteone spp. and Scoloplos armiger) had less numbers in the plots where detritus was buried than in the controls. These findings showed that burial of macroalgal detritus does not represent a major source of variation at the scales examined. It is suggested that in these sediments, recycling of detritus is fast and it buffers the effects of excess organic matter in the system.     

Iron Additions Reduce Sulfide Intrusion and Reverse Seagrass (<Emphasis Type="Italic">Posidonia oceanica</Emphasis>) Decline in Carbonate Sediments

Abstract We conducted a 2-year in situ experiment to test the capacity of iron additions to reverse the decline experienced by a Posidonia oceanica meadow colonizing carbonate, iron poor sediment. Iron additions improved the sediment conditions that support seagrass growth by decreasing the sediment sulfide concentration and sulfate reduction rates, and decreased sulfide intrusion into the plants. Iron additions for 2 years did not significantly change survivorship of shoots present at the onset of the experiment, but significantly increased shoot recruitment and survivorship of shoots recruited during the experiment. After 2 years, iron additions reversed seagrass decline and yielded positive growth rates of shoots relative to control populations where seagrass continued to decline. This research demonstrates that seagrass decline in carbonate sediments may be reversed by targeting critical processes such are sediment sulfide pools and seagrass nutritional status, controlling the functioning of the ecosystem.     

Experimental Evaluation of the Restoration Capacity of a Fish‐Farm Impacted Area with Posidonia oceanica (L.) Delile Seedlings

Marine aquaculture is an activity that has induced severe local losses of seagrass meadows along the coastal areas. The purpose of this study was to evaluate the capacity of an area degraded by fish‐farm activities to support Posidonia oceanica seedlings. In the study site, a bay in the southeast coast of Spain where part of a meadow disappeared by fish‐farm activities, seedlings inside mesh‐pots were planted in three areas. Two plots were established in each area, one in P. oceanica dead matte and another inside a P. oceanica meadow. To evaluate if sediment conditions were adequate for the life of the seedlings, half of them were planted in direct contact with the sediment and the other half were planted above the surface of the sediment in each plot. Monitoring during 1 year showed that there were large differences in seedling survival between the dead matte and the P. oceanica meadow. While seedlings planted in dead matte had a high survivorship after 1 year (75%), seedlings planted in P. oceanica progressively died (survivorship of 20% after 1 year). The average leaf length of the seedlings surviving in the two substrata was not different, but the leaf area per seedling was lower in the seedlings growing inside the P. oceanica meadow during most part of the year. Seedling survivorship and vegetative development were not affected by the level of planting and suggest that the sediment conditions are adequate for the life of P. oceanica seedlings.     

Seagrass Restoration Enhances “Blue Carbon” Sequestration in Coastal Waters

Seagrass meadows are highly productive habitats that provide important ecosystem services in the coastal zone, including carbon and nutrient sequestration. Organic carbon in seagrass sediment, known as “blue carbon,” accumulates from both in situ production and sedimentation of particulate carbon from the water column. Using a large-scale restoration (>1700 ha) in the Virginia coastal bays as a model system, we evaluated the role of seagrass, Zostera marina , restoration in carbon storage in sediments of shallow coastal ecosystems. Sediments of replicate seagrass meadows representing different age treatments (as time since seeding: 0, 4, and 10 years), were analyzed for % carbon, % nitrogen, bulk density, organic matter content, and ²¹⁰Pb for dating at 1-cm increments to a depth of 10 cm. Sediment nutrient and organic content, and carbon accumulation rates were higher in 10-year seagrass meadows relative to 4-year and bare sediment. These differences were consistent with higher shoot density in the older meadow. Carbon accumulation rates determined for the 10-year restored seagrass meadows were 36.68 g C m^-2 yr^-1. Within 12 years of seeding, the restored seagrass meadows are expected to accumulate carbon at a rate that is comparable to measured ranges in natural seagrass meadows. This the first study to provide evidence of the potential of seagrass habitat restoration to enhance carbon sequestration in the coastal zone.     

Nutrient dynamics in 3 morphological different tropical seagrasses and their sediments

Seasonality of nutrient dynamics in three morphologically different seagrass species and their sediments was examined for 1 year between November 2006 and November 2007 at four sites in the Andaman Sea, Thailand. The smaller species, Cymodocea serrulata and Halophila ovalis, showed major seasonal variation in shoot density, above- and belowground biomass, much more than expected from seasonal changes in water temperature and light conditions. All parameters showed minimum values in the dry season due to desiccation during neap tides. In contrast Enhalus acoroides showed less seasonal variation. Only limited seasonality was found in tissue N content of all species, whereas tissue P content responded to the low P concentration in the water column during the wet season. There were no differences in sediment conditions among species, and nutrient pools were generally low. Furthermore there were no significant spatial differences in seagrass and sediment nutrient dynamics, despite varying anthropogenic activity at the study sites, reflecting the oligotrophic conditions in this region.     

Growth responses of Zostera capricorni to estuarine sediment conditions

This study comprised (1) a field survey of intertidal seagrass (Zostera capricorni) biomass, cover and photosynthetic potential and sediment characteristics at a range of contrasting sites in three New Zealand harbours, and (2) a microcosm experiment comparing plant responses to sediments from extant versus historical seagrass sites. The field survey showed that the sediment physico-chemical characteristics were generally consistent with the limited previous reports for Zostera environments, although the total P concentration range was higher (0.08–0.72 mg P g⁻¹). Overall, 52% of variation in seagrass cover was explained by sediment water content (R = 0.54) and organic content (R = −0.56). Twenty-two percent of variation in seagrass biomass was explained by sediment total P and redox potential (both R = −0.35). Intra-harbour seagrass–sediment relationships were more significant (explaining up to 82% of plant variation) but harbour-specific. In the microcosm experiment, threefold higher Z. capricorni biomass was maintained on extant than historical sediments but not conclusively linked to measure sediment characteristics. Overall, the results of this study demonstrate that significant relations can exist between estuarine sediment conditions and Z. capricorni growth responses, and suggest that detrimental change in sediment conditions may be a contributing factor in seagrass decline.     

Growth responses of Zostera capricorni to estuarine sediment conditions

This study comprised (1) a field survey of intertidal seagrass (Zostera capricorni) biomass, cover and photosynthetic potential and sediment characteristics at a range of contrasting sites in three New Zealand harbours, and (2) a microcosm experiment comparing plant responses to sediments from extant versus historical seagrass sites. The field survey showed that the sediment physico-chemical characteristics were generally consistent with the limited previous reports for Zostera environments, although the total P concentration range was higher (0.08–0.72 mg P g⁻¹). Overall, 52% of variation in seagrass cover was explained by sediment water content (R = 0.54) and organic content (R = −0.56). Twenty-two percent of variation in seagrass biomass was explained by sediment total P and redox potential (both R = −0.35). Intra-harbour seagrass–sediment relationships were more significant (explaining up to 82% of plant variation) but harbour-specific. In the microcosm experiment, threefold higher Z. capricorni biomass was maintained on extant than historical sediments but not conclusively linked to measure sediment characteristics. Overall, the results of this study demonstrate that significant relations can exist between estuarine sediment conditions and Z. capricorni growth responses, and suggest that detrimental change in sediment conditions may be a contributing factor in seagrass decline.     

Assessing effects of fishing prohibition on Posidonia oceanica seagrass meadows in the Marine Natural Reserve of Cerbère-Banyuls

The potential of alleviated fishing pressure measures established at the Marine Natural Reserve of Cerbère-Banyuls to affect phenological characters of P. oceanica, the main canopy-forming seagrass, was studied. Our results show differences in some leaf parameters between meadows under fishing prohibition measures compared to those without. In addition shallow P. oceanica meadows inside MPAs had lower non-structural carbohydrate content, yet are able to maintain themselves and, moreover, with an increased density. On the other hand, sexual reproduction was reduced inside protected areas.     

Seagrasses are negatively affected by organic matter loading and Arenicola marina activity in a laboratory experiment

When two ecosystem engineers share the same natural environment, the outcome of their interaction will be unclear if they have contrasting habitat-modifying effects (e.g., sediment stabilization vs. sediment destabilization). The outcome of the interaction may depend on local environmental conditions such as season or sediment type, which may affect the extent and type of habitat modification by the ecosystem engineers involved. We mechanistically studied the interaction between the sediment-stabilizing seagrass Zostera noltii and the bioturbating and sediment-destabilizing lugworm Arenicola marina, which sometimes co-occur for prolonged periods. We investigated (1) if the negative sediment destabilization effect of A. marina on Z. noltii might be counteracted by positive biogeochemical effects of bioirrigation (burrow flushing) by A. marina in sulfide-rich sediments, and (2) if previously observed nutrient release by A. marina bioirrigation could affect seagrasses. We tested the individual and combined effects of A. marina presence and high porewater sulfide concentrations (induced by organic matter addition) on seagrass biomass in a full factorial lab experiment. Contrary to our expectations, we did not find an effect of A. marina on porewater sulfide concentrations. A. marina activities affected the seagrass physically as well as by pumping nutrients, mainly ammonium and phosphate, from the porewater to the surface water, which promoted epiphyte growth on seagrass leaves in our experimental set-up. We conclude that A. marina bioirrigation did not alleviate sulfide stress to seagrasses. Instead, we found synergistic negative effects of the presence of A. marina and high sediment sulfide levels on seagrass biomass.     

Long-term manuring and fertilization effects on soil organic carbon pools under a wheat–maize cropping system in North China Plain

The effects of organic manure and chemical fertilizer on total soil organic carbon (C _T), water-soluble organic C (C _WS), microbial biomass C (C _MB), labile C (C _L), C mineralization, C storage and sequestration, and the role of carbon management index (CMI) in soil quality evaluation were studied under a wheat–maize cropping system in a long-term experiment, which was established in 1989 in the North China Plain. The experiment included seven treatments: (1) OM: application of organic manure; (2) 1/2OMN: application of half organic manure plus chemical fertilizer NPK; (3) NPK: balanced application of chemical fertilizer NPK; (4) NP: application of chemical fertilizer NP; (5) PK: application of chemical fertilizer PK; (6) NK: application of chemical fertilizer NK; and (7) CK: unfertilized control. Application of organic manure (OM and 1/2OMN) was more effective for increasing C _T, C _WS, C _MB, C _L, C mineralization, and CMI, as compared with application of chemical fertilizer alone. For the chemical fertilizer treatments, balanced application of NPK (treatment 3) showed higher C _T, C _WS, C _MB, C _L, C mineralization, and CMI than the unbalanced use of fertilizers (treatments 4, 5, and 6). The C storage in the OM and 1/2OMN treatments were increased by 58.0% and 26.6%, respectively, over the NPK treatment, which had 5.9–25.4% more C storage than unbalanced use of fertilizers. The contents of C _WS, C _MB, and C _L in organic manure treatments (treatments 1 and 2) were increased by 139.7–260.5%, 136.7–225.7%, and 150.0–240.5%, respectively, as compared to the CK treatment. The CMI was found to be a useful index to assess the changes of soil quality induced by soil management practices due to its significant correlation with soil bulk density and C fractions. The OM and 1/2OMN treatments were not a feasible option for farmers, but a feasible option for sequestering soil carbon, especially for the OM treatment. The NPK treatment was important for increasing crop yields, organic material inputs, and soil C fractions, so it could increase the sustainability of cropping system in the North China Plain.